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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG

Basic information

species Zea mays
transcript GRMZM2G110983_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagatt--cgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG-----
                                       |    |||   || | | |||    ||          |    ||  ||   | ||  | | |  ||  ||| ||| || | | |   |          ||||       |   |||||||| || || ||||||||| |||||||||||||||| ||  |||||||||| ||||| || ||||||||||| ||||| ||||     
--------------------------------------attggtctgg--ctagtaggtgtcatgggtaaactaaagaatctcagtgtaggtttcccattccttctatttagcttatttggtgacttggtatctacacagGG-----TGAATATGTCGACGCCAGCAAGGAAGAGGTTGATGAGGGATTTCAAACGACTGATGCAGGATCCTCCAGCTGGCATAAGTGGGGCCCCACAGGACAAC

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatcct-tttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
                                          |  || |  |   | ||    ||      || |  |  |   |   | ||||  | | |  || ||    || |  |   | || |  ||  | || |      ||   |||||||||||||| ||||||||||||||||| || |||||| || ||   || ||||| || || || || || || ||||| ||||   
----------------------------------------ttatgtggtgttgctatgttggaggcttttttgcccccttaaatacactcgattgattcaagtctattcttttccttattgtgagtgttggtttttcaagGTGG--CGACAATGTCGACTCCTGCTAGGAAGAGGCTGATGAGAGACTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGGATCAGCGGTGCCCCCCAGGATA

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatg-tcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
                                            ||  ||    |||   ||    |    |  |      |   | ||   | |    || |   ||        ||||  ||||  || | | |    |  |   |  |||||||||||| || |||||||| |||||||||||||| ||  | |||   || || ||||| || ||||| ||||| || || || |   
------------------------------------------ttcttgtttactcactcactctccctttctatctcaattttttttatccgtgcacatgagctgattactattgtttgaattgtacttgattgggataaagGAGGTGAAGATGTCGACTCCGGCTAGGAAGAGACTGATGAGGGATTTTAAAAGATTGCAACAAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCAAGACA

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG
    | | ||| ||      ||   |   |   | | | |  | ||  || |||    || ||    |            || || | ||  | | |    | ||| |||||   |||    | | || ||             |  |  |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||      
----tctcttctcttgttccttaaccatctaactcaccttatatctccttgttgt---tgttgaaaagaaa---------attgaagttatttccatttt-ttcttgtggct---gttagTTTTTCTAGGTG------------CTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCC------

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
             |  ||| |   | ||  ||||  |  |||      |||||    ||  |         |    |   || || | ||  | |||    || || |||||   ||||   | | || ||         | |||     |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || ||||| || || || || || || || || ||||   
------------ttggaatctgaattgacctgttggttatgc------ttcttaatagttttt--------taatagaaaattgaagttatttccgttttctctttgtggct---gttggtttttctagGT--------GATATC----AATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCGCCTGCAGGAATCAGCGGGGCACCTCAGGATA

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
                                ||  ||||  |||    |||  | |    |    |    ||  |  |  | ||  | | | | |   | |  ||     |  | ||| ||    ||  |  |  |||     |  |  |||||||||||||| ||||||||||| ||||| ||||||||| || ||   || |||||||| || || || ||||||||||| ||||   
--------------------------------ttgttccttaacca---tctaactcaccttatatctccttgttgttg--ttgaaaagaaaattgaa-gttatttccattttttcttgtggctgttagtttttctagGTG---CTAGCAATGTCGACTCCTGCTAGGAAGAGGCTCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATA

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G14400.1 (Arabidopsis thaliana), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgat-gatagattcgtgcgatccttttggctcatg----ttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG
                                               | | | |||   |          || |       | ||| ||||||     | || | |    | | |||    ||  |  |  | |||     || || |   | |||||||||| || || ||||||||| | ||||||||||||||| |||||  ||| ||||| || || || || ||||| || || ||||
-------------------------------------------agcaactttagcatacgtaaatcgttagtagtaatttctagattgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagAAAGAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGG

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G14400.2 (Arabidopsis thaliana), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgat-gatagattcgtgcgatccttttggctcatg----ttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG----
                                               | | | |||   |          || |       | ||| ||||||     | || | |    | | |||    ||  |  |  | |||     || || |   | |||||||||| || || ||||||||| | ||||||||||||||| |||||  ||| ||||| || || || || ||||| || || ||||    
-----------------------------------------------actttagcatacgtaaatcgttagtagtaatttctagattgatagaggttcgagaccttaaaaggtgatgaatatttggtgggttttgtttattagaaagAAAGGAGGATGTCGACGCCAGCAAGGAAGAGGTTAATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCGGGTATTAGTGGTGCTCCACAGGACAA

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G02760.1 (Arabidopsis thaliana), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG
                    ||| | |     || |    |     |||  |||||  | |    ||   | |   |  | |   ||| | | |     | |     ||| |     || | | |     | | | | ||  |     ||||||||||||| |||||||||||  ||||||||||||||||| |||||  ||| ||||| || || || || ||||| || || || |
--------------------ttgcttggcagattcaaatggtttgagataattgcatatcc--aagctctgagatagttggtttttgaaatactgtaatggt-----tggtt---actgggatttg---atagAGTAAGAGAA-----GGATGTCGACTCCAGCGAGGAAGAGATTGATGAGGGATTTCAAGAGGTTGCAGCAAGACCCACCTGCAGGAATTAGTGGTGCTCCACAAG

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 2
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
                        | |||| | ||| | ||||    | | ||| |     ||   |   |    |    |  ||||||      |     |  |||||| |        ||  | | | | |   |||       | ||||||||||||| || ||||||||||| ||||||||||||||| |||||   ||||| || || || ||||| ||||| || || || |   
------------------------ttgagt-gataaacatgcattatactattgta---attgactcactgcattgtttaa--gatgattaccaagcaatgttgttttggtt--------ggcttctctttggaatagGCGG---TGAGGATGTCGACTCCAGCCAGGAAGAGGCTCATGAGGGATTTCAAGAGGTTGCAACAGGATCCACCTGCAGGCATCAGTGGTGCTCCTCAAGACA

upper sequence: GRMZM2G110983_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 1
gtagttttttccctcaaattttgttcgagttgttaatcctgcacctgattcttgcacgtgctggggcggggtggcggcggatcgatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG---
          |     |||    ||    || ||  |  ||     |||| ||  | ||  |  |  || |  | | |  |||||      ||  |   |||   |||||||         |   || | |   || |        | |||||||||| ||  | ||||||||||||||||||||||||||| || |   ||| || ||||| || || || ||||| || || || |   
----------ctaatgaatgaaatttagtttcttgtttgtg-----gatttttatatgttattagctggagaag-gaccaatcga------atctgattgat---tttggct---------ggaaattttttagGCGG-------TGAGGATGTCGACCCCATCAAGGAAGAGGCTGATGAGGGATTTCAAGAGGCTTCAGCAAGATCCTCCTGCTGGTATCAGTGGGGCACCCCATGACA

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|211409051|gb|FL320424.1|FL320424
EST:     ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGAT                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|211220711|gb|FL342801.1|FL342801
EST:     ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGAT                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|211116612|gb|FL350324.1|FL350324
EST:     ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGAT                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|211110600|gb|FL338769.1|FL338769
EST:     ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGAT                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|211352621|gb|FL361436.1|FL361436
EST:     ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGAT                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|211149404|gb|FL319863.1|FL319863
EST:     ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGAT                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGANGCTGATGAGGGATTTC
genomic: ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|211165158|gb|FL324135.1|FL324135
EST:     ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGAT                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
EST: gi|211193874|gb|FL364458.1|FL364458
EST:     ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGAT                         GAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC
genomic: ACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTC

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), 48 (downstream exon)
Score: 274

ATATGATTGATTAGTCCGTATCGTCCTAGCTGGGATGGATGCCCCGATCCACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

ATATGATTGATTAGTCCGTATCGTCCTAGCTGGGATGGATGCCCCGATCCACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 374

ATATGATTGATTAGTCCGTATCGTCCTAGCTGGGATGGATGCCCCGATCCACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 328

ATATGATTGATTAGTCCGTATCGTCCTAGCTGGGATGGATGCCCCGATCCACCAATTCTGTTGCGGATTTGTTCGCTCTGTGGTTCCGGTGGTAGCAGATgtagtttttt ... tgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgatagattcgtgcgatccttttggctcatgttgaggtgtatatgtcgtgcagGAACATCCGGGGATGTCGACTCCTGCGAGGAAGAGGCTGATGAGGGATTTCAAGCGGTTGATGCAGGACCCTCCGGCCGGCATAAGTGGCGCCCCGCAGG
                                       tgtatat  TA-rich tract