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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC

Basic information

species Zea mays
transcript GRMZM2G171484_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g73160.1 (Oryza sativa), 3'ss of exon 2
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                        | ||| ||| ||||  |  |   |||     |   |  | || |    ||     ||    || ||    |          ||  ||  || |      ||||||| ||||   ||||||| ||  | ||||||||||||||||||||||||||||||||||| ||| |||| ||||||||| ||||||||||||||||||||||||||||||||||
-----------------------------------------------------acatgttttatttgatt-ggtcatgtatttgctgaaggcctgaatga-tggtacctttatttgttatgagttgaa---------gtgctaatttaa------ttcaactatatg---cagAGGGAGTCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCAAAGGTTGATGTGCCCAACTTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G02070.1 (Glycine max), 3'ss of exon 2
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcc-cgtccttgtcttagattgagaaccgttcaactttatgt---tgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                                                                  |||     || | ||    |  |    | | | |||    |  | |   | |    | ||   ||| ||||   ||||||||| |||   | ||| |||||||||| |||  |||| ||||||||  || |||||||||| || ||| ||||||||||||| |||||||| ||||||||
-------------------------------------------------------------------------------------------------gtaggtgccttagaatttcattggggttacgtctcgttgaagaatgaatcttaccttcttttttcttaatgtcggtgcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATTTGGCGAAGCACCCTGAGATTGACGTGCCGAATCTGCAGGTGATTAAGCTGATGCAGAGTTTCAAGTC

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagc-aatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC--------------------
                                                                                               | ||||  || |||    | || | |               |||| ||| | |   ||  ||     | | || | ||||||| |||   | ||| |||||||||| ||| ||||| ||||||||  || |||| ||||| || ||| ||||||| ||||| |||||||||||||| ||                    
--------------------------------------------------------------------------------------------gtccgttagttaacatt---gttgtctcctcttgtgctttacagttgtgttaaaattgtaag-gtgtgtgtgtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G02410.2 (Glycine max), 3'ss of exon 2
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagc-aatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                                                               | ||||  || |||    | || | |               |||| ||| | |   ||  ||     | | || | ||||||| |||   | ||| |||||||||| ||| ||||| ||||||||  || |||| ||||| || ||| ||||||| ||||| |||||||||||||| ||
--------------------------------------------------------------------------------------------gtccgttagttaacatt---gttgtctcctcttgtgctttacagttgtgttaaaattgtaag-gtgtgtgtgtttgattcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATC

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G37470.1 (Glycine max), 3'ss of exon 2
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                                      ||| | ||    ||   || || |  || | |    ||||    |  |||| | |             |||||  ||      ||||    |||||| ||||||||| |||   |  || |||||||||| |||  |||||||||||||  || | |||||||| || ||| ||||||||||||| |||||||| ||||||||
---------------------------------------------------------------------gtaggtgccttagcatttatcacga--atcatcttcgttcgttagggttacgtctcgttgaacaatgaatcttacctt-----tcgttggtgtttatggtgcagAGGGAGTTTGCTTCGCGAAGAAGGACTTCAATTTGGCCAAGCACCCTGAGATCGACGTGCCGAATCTGCAGGTGATTAAGCTGATGCAGAGTTTCAAGTC

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G43110.1 (Glycine max), 3'ss of exon 2
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                                                               | ||||  |   | |  || | |    |   |   ||    ||| ||| ||||  |   |      | | || | ||||||| |||   | ||| |||||||||| ||| ||||| ||||||||  || |||| ||||| || ||| ||||||| ||||| |||||||||||||| ||
--------------------------------------------------------------------------------------------gtccgttagttaacattgtctcctcttgtgcttta---cggttgtgt-ttaaattgtaacgtg------tgtttgattcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATCTGGCGAAGCACCCGGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATC

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G25740.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacatt-acaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                                       | ||| |  || ||  ||| |  | |     |  || || | | || ||       |    ||     |  || ||    |    |   |||   | | | |||||| ||    | ||| |||||||| | ||| ||  | ||||| ||   | |||| || || |||||| | |||||||||||||||||||| ||||||||
-----------------------------------------------------------------------atataactgttgagggatttattatctagtactgtactcag-ttgtctagagaaagaatttgtgtggatactaaatgatca--tatcttactgggtttcgtagAGGGAGTATGCTTTGCTAAGAAGGATTTCAATCTCCCAAAGCATCCGTTGATTGATGTACCAAACCTGCAAGTGATTAAGCTCATGCAGAGTTTCAAGTC

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0050g01160.t01 (Vitis vinifera), 3'ss of exon 2
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                          ||||||||| |||     |  ||  | |  |||  ||||  |  ||  || ||||| |||            | ||  | ||||| ||     |   | ||    | ||| |||||||| |||   ||||| |||||||||||||| || || || |||||| |  |||| || || || ||| ||||||||||| | ||||||||||| |||||
----------------------------------------------------caccgttttcattagttttc----ctcatctatattttattagcaacaa-aacgtt-ggatcatgt----------ttcatctatttcttatatgtgatattttgca----tgtgt-gcagAGGGAGTTTGCTATGCAAAGAAGGACTACAATCTTGCAAAACACCCCGAAATTGATGTTCCAAATCTGCAGGTGATTAAGTTGATGCAGAGCTTTAAGTC

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP00807 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtgagctcct-----tctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcat-tagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtct-tagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG---CTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
||||||  |      | | |  ||||   |  ||    | | |  || ||    | | |           |||       |  |    || |   | |  ||    ||  | |||||  ||   |         ||  |   ||  |  | |     |   | ||   | |  |  |||||||| || ||  | ||  ||||||||| ||||||     |||||||  ||   |  | ||||||||||||| |||| |||||||||||||||||||||||   
gtgagcatcagttggtatgcgacctcggtgttcgcgttctttgaggc-ccggggacatggacgccgggcctagcgacgcttgtcggcgcacagcctgcg-gcgcgcgctttcttcgg-ccgcaaatttatttccccaatgtatgcttacacacctgtatttgctcg-ttgtgcgc-gcagAGGGTGTCCTTCAGGCGGAGAAGGACTTCAACCTCAAGGAGCACCCGGAGATCCCCGGCGTGCCCAACCTGCAGGTCATTAAGCTCATGCAGAGCTTCAA---

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29946 (Selaginella moellendorffii), 3'ss of exon 1
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                                                        | |   |   ||||       ||  ||    || | || ||   | ||  ||  |||||     |    ||| | |  |  |||||||| || || || ||||||||||||||||| ||  ||||||||||  || | || || ||||| ||  ||||||| |||||||||||||||||||||||
---------------------------------------------------------------------------------------gtgaggggatctagcttctcctggcgcgctcgcg-ctcacgcat-ttctaatccgagattt----ctccccaattgttcggcgcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC

upper sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25099 (Selaginella moellendorffii), 3'ss of exon 1
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttc--aactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                                                                                        |    |||||  |  || | ||   |   | || |  ||    ||||    | |  || | |  |  |||||||| || || || ||||||||||||||||| ||  ||||||||||  || | || || ||||| ||  ||||||| |||||||||||||||||||||||
-------------------------------------------------------------------------------------------------------gtgaggggatctagctcg-cgcatttctcccttttttctaatccgagatttctccccaattgttcggcgcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211053112|gb|FL123928.1|FL123928
EST:     GATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: GATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|78544011|gb|DV621509.1|DV621509
EST:     ATCATCTCCAAGAAGAA-CGCCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCG-CCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|60339885|gb|DN206858.1|DN206858
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|67035082|gb|CO463615.1|CO463615
EST:     ATCCTCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGG-TCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTC-TATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG
EST: gi|28930975|gb|CB334336.1|CB334336
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|28873901|gb|CB329830.1|CB329830
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211053106|gb|FL123922.1|FL123922
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211023430|gb|FL440278.1|FL440278
EST:     AAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: AAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211056047|gb|FL123934.1|FL123934
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|18384945|gb|BM418144.1|BM418144
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGAGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|193503176|gb|AM937588.1|AM937588
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|76921190|gb|DV168486.1|DV168486
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|14203665|gb|BG837342.1|BG837342
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211056057|gb|FL123944.1|FL123944
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211053113|gb|FL123929.1|FL123929
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|67030453|gb|CO459202.1|CO459202
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGG-TCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTC-TATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG
EST: gi|211053108|gb|FL123924.1|FL123924
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|32914955|gb|CF019767.1|CF019767
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|32825443|gb|CD965165.1|CD965165
EST:     GATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: GATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|14701474|gb|BI233892.1|BI233892
EST:     ATCATCT-CAAGAAGAACC-CCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|87298799|gb|DY470802.1|DY470802
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|67017230|gb|CO445979.1|CO445979
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGG-TCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTC-TATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG
EST: gi|211053115|gb|FL123931.1|FL123931
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|32914944|gb|CF019756.1|CF019756
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|31353380|gb|CD437737.1|CD437737
EST:     GATCATCTCCAAGAAGAACCGCCGCGAGATCTCCTAGAACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: GATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211053110|gb|FL123926.1|FL123926
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|29130033|gb|CB380737.1|CB380737
EST:     CCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: CCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211056056|gb|FL123943.1|FL123943
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAAANCTGGCCAAGCACCCCAAG
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAAC-CTGGCCAAGCACCCCAAG
EST: gi|211056051|gb|FL123938.1|FL123938
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|16745968|gb|BM032398.1|BM032398
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|37381614|gb|CF627703.1|CF627703
EST:     ACCGCCGCGAGATCTGCAAGTACATCTCCCATG                         AGGGGG-TCTTGTATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG
genomic: ACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTC-TATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAG
EST: gi|22489259|gb|BU049182.1|BU049182
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|31355636|gb|CD439993.1|CD439993
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211053117|gb|FL123933.1|FL123933
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211056058|gb|FL123945.1|FL123945
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211053111|gb|FL123927.1|FL123927
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211056054|gb|FL123941.1|FL123941
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|32863602|gb|CF003284.1|CF003284
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211023429|gb|FL440277.1|FL440277
EST:     AGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: AGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211053114|gb|FL123930.1|FL123930
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211056053|gb|FL123940.1|FL123940
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|76011994|gb|DT939164.1|DT939164
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|18384613|gb|BM417812.1|BM417812
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGAGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|60338236|gb|DN205209.1|DN205209
EST:     GAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: GAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|18384615|gb|BM417814.1|BM417814
EST:     ATCATCTCCAAGAAGANCCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211056050|gb|FL123937.1|FL123937
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|31356366|gb|CD440723.1|CD440723
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
EST: gi|211056049|gb|FL123936.1|FL123936
EST:     ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATG                         AGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC
genomic: ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 64

ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 28

ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 88

ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACATCTTCCATGgtgagctcct ... tatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC
                                        aactttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctccttctcctccctcttcgcccgtccccctaggcgcgcccaatataagattatttcattagatttagataccaattcagacattacaagcattagcaatattcggatcgtgtacgacccaagcccgtccttgtcttagattgagaaccgttcaactttatgttgcagAGGGGGTTCTATATGCCAAGAAGGACTACAACCTGGCCAAGCACCCCAAGCTTGACGTGCCCAACCTGGAGGTGATTAAGCTCATGCAGAGCTTCAAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT