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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG

Basic information

species Zea mays
transcript GRMZM2G169773_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagt------ttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                                                || ||  ||||  |||    ||||  | ||| ||   |  | |      |||| ||  ||  |      |   || |||  | |    |||   ||     | ||||||||||||||||| |||||||||||||| || ||||| |||||||| || ||||| || ||||||||||||||    |||||||||||||||  | | |
------------------------------------------------------------ccctaagattttgttcttgt----tgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaact-tggccgtttgaaa-----tgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattat-tgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG-
                                                           ||   | |||  |    ||||  ||  || ||||   |||||| |||||      | |        |||   |||||    ||||| || | | || || || ||||||||||| |||||||||||||| ||||| || |||||||   | ||||| ||||| ||  | ||  | |||| |   ||  | | | |  || || ||  
----------------------------------------------------------gtttttatcatattagcactgtaacac-caacata--ttctcttgaagtt------actt-------gagtctttttgtttgattatgtgcttttaaatt-ttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGC-ACTTACA

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgttt-cagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                            || |    | | |  ||   ||| |     |  | |      ||||  |    |  ||| | |  ||    |||   | || |  |   |  |   | | ||  | ||   |  | | |||||||||||||||||||||||||| ||||| || ||||| |||||||| || || || ||| | || || ||||||  |||  | ||||  | | | |  |
--------------------------------------------gtttgattacacttcttg--aactttacaatcatcttaagcacatc-caccaccattttgaatgacatgatttccttacgaca--tacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                                                             | | | ||   || ||| ||||    | | | || |   |       || | | | ||     |   ||  | |  |   |   ||||||||||||||||||||||| || |||||||| ||||||| ||||| ||| || || || |  || || ||||||   ||  |                 
----------------------------------------------------------------------------gtttttaata-gtcctaaactctacc-atggtgcattctcttggctctagtgttttctttgttgacatttaatttatatacg---cagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgttt-cagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                                           || | || ||     |    | |  || |   |     | |||     ||  | |   |   |  | ||    | |    | || |||||      |||  | ||||||||||| |||||||||||||| ||||| || ||||| ||||||||||  ||||| ||  | || ||  |||||  |||    |||             
----------------------------------------------------------gtttg-aatatacatctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgttcactttttttgttt---gtttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                          | |  ||| | ||||      |    ||  || | |||| ||||         | |       ||| || ||  | | | || | |  || | |    |    |  ||||   |  |||                ||||||||||||||||||||||| || ||||| || || || |||||||| || ||||| ||  | || ||  |||||  |||  | ||||  | |   || |
-------------------------gtttgactacacttcttgaactttccaatcatcttaagca-catg-caccagcattttgaatgccatgatttccttatgaattaccac-ataccaactcactatttctttggtttgctata---------------cagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                              ||  | |||| |||  | |      | ||| ||     || |  |||      |||     ||  | |   |   |  | || |  | |     | | ||  | ||   |   | ||||||||||| |||||||||||||| ||||| || ||||| ||||||||||  ||||| ||  | || || |||||| ||||  | ||||| |      |  
----------------------------------------------gttcgaatatacatctgaa------tatttttggaaagtggaa-ata------cttagcactttgactgaacataaccaaagttaatgtt---cactttttgtttgg-ttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT1G03550.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattat--tgttctgaacttg--tttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                                                      || | ||    || |  |    |   | | |      |  || |   || |||   | |||||||   |    ||   || |   ||| |  ||||||||||||||    |||||||| || ||||| |||||||||||||||||||| || ||  |        |  ||| |  |||  | |||   |   ||    
----------------------------------------------------------------------gtttctcaacttcttctactccagaatttatcagcactgtaaat-cacttgaatccatctgtttttctaacccatgacgtgcaatactcgactttcagCAAGTATATGCATACTTCCGAGGGAGTGGCAAAGCTGCAGAGATGAAGCGTGAAGCTACAAAATCGACCTTGATGCGTGCACTATGAAGAAATCACTCTT

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT1G11180.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaatta-ttctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                                                        || ||| ||  |   |||| |  |  ||| |   |    ||   ||||  |  | | || |||| | | ||| |  || ||       | ||||||||||||||||||||| | ||||| |||||||| |  || ||||  || || || ||  | || || |||||   |||| | |||   |       | 
------------------------------------------------------------------------gtctctttccta---atcagatacaatctctggatcgatataggttctgaagcaaaactcttttta-acatt-tgattgtg-------tgcagCAAGTATACATGTACTTCAGAGGAAGCGGAAAAGCGGATGATATGAGACGGGATGCTGCAAGAGGAGCCATGAGAGCTGCCATATGAGGCAAATGTAAAT

upper sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaa-catggtgtttctgtctcatgcatcataatctctcttta-agtttcaattattctagaagagagctgttttgagatattattgttctgaacttgttt-cagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                              ||     |  || ||  ||  | |  |  |   |    | ||||    | ||||  | | ||  | ||| || |           ||||    | |  | ||||| | | || |||| ||||||||||| ||||||||||| || ||||| ||||| || ||||||||||| || || ||  | || || ||||||  ||| || | |    || |     
----------------------------------------------gtccaacttctctttcccattcctaataatcacgg--aaagcatagctacctctgctaataggatgaatcatgc-----agctcttgttcactgtttctgttgtt-tcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC

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|76293307|gb|DV032875.1|DV032875
EST:     GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG                         CCAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGAT
genomic: GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGAT
EST: gi|88749197|gb|DY533338.1|DY533338
EST:     GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG                         CAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
genomic: GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
EST: gi|166600640|gb|EG168684.1|EG168684
EST:     CATCGTTGTCATTCAG                         CAAGTATACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGA
genomic: CATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
EST: gi|76293306|gb|DV032874.1|DV032874
EST:     GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG                         CAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
genomic: GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
EST: gi|8368017|gb|BE050962.1|BE050962
EST:     TATTTGGAATGCTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG                         CAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
genomic: GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
EST: gi|211151165|gb|FL467100.1|FL467100
EST:     GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG                         CAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
genomic: GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
EST: gi|78115058|gb|DV533446.1|DV533446
EST:     GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG                         CAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
genomic: GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
EST: gi|91049868|gb|EB160286.1|EB160286
EST:     GATTTGGAATGTTTTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG                         CAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
genomic: GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
EST: gi|78077113|gb|DV505547.1|DV505547
EST:     GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG                         CAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA
genomic: GATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGA

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), 46 (downstream exon)
Score: 79

ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 163

ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 167

ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 171

ATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAGgtgggtatca ... cttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
                                             cttgtttc  CT-rich tract
                      ttttgagatattatt  TA-rich tract