Sequence
atgc intronic sequence ATGC exonic sequencegtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
Basic information
species | Glycine max |
transcript | GLYMA11G38110.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
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--------------------------------------------------nnnnnnnnnnnnnnnnnnncacattactatttgagttttggta---gctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
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-------------------------------------------------------------------gtgagaacaatgttacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataacaaaacaagttttga-ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttct--ttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
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--------------------------------------------------tgaatggaacatcaaaatgtccatggaaattctcagcattgtgtat-caaccatgttcattcttttagttatatgtcattt-tgaatcatatt---actgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA-----------
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---------------------------------------------------------------gtaagaaatgctgttttttctagggcttctc--gcaatgtaatat-tcgcaatgaggaagctaataatgt---gaattttcgtttt-tagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgtt-atgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
|| || | | ||| || | | | || || ||| || | | | ||| || | ||| | | ||| | | | | ||| || |||||||||||||||| || |||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| || ||||| |||||||| | |
---------------------------------------------------gattggtttctcaaa--ttgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagtttctaaaat-tttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
upper sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
||||| ||| | || | | || || | | | | | | | | | | | | ||| | | | | | | | ||||||||||||||||||||||||||| ||||||| ||||| ||||| || | ||||| || || ||||| | || ||||| || | |
---------------------------------------------acaatttttctgtttgggggcagcagagatgaactttacctactggtttgt----ctcctctggcagaccaattgacgtt----gcttcccctgctgaactgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
ttttaac putative branch site (score: 2)
tttgtatgttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA