Sequence
atgc intronic sequence ATGC exonic sequencegtatagttattcaattttaggatgcatttgtttaaccaagcataatgtagagatacaaaattgtaacattttcctcggtcaaatttcttgtatcttttaattaacttgttgtatttgcttaatcaggaagtttataatctattcattgcaacaataagtaattaatattatcccttttgttctttcatttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
Basic information
species | Glycine max |
transcript | GLYMA08G24160.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01480.t01 (Vitis vinifera), 3'ss of exon 4
gtatagttattcaattttaggatgcatttgtttaaccaagcataatgtagagatacaaaattgtaacattttcctcggtcaaatttcttgtatctttt-aattaacttgttgtatttgcttaatcaggaagtttataatctattcattgcaacaataagtaattaatattatcccttttgttctttcatttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
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-------------------------------------------------------------------------------------gtatatatattttgaacctaatcatcatcctaacctcataaatgggcttggag-ctttgaagtatgaaaatggcttatgtacatggc---------------------agAATGAAGATGGTGGGTGGGGATTGCATATTGAGGGACACAGCACAATGTTTTGTACAACACTCAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCGCG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 6
gtatagttattcaattttaggatgcatttgtttaaccaagcataatgtagagatacaaaattgtaacattttcctcggtcaaatttcttgtatcttttaattaacttgt-tgtatttgcttaatcaggaagtttataatctattcattgcaacaataagtaattaatattatcccttttgttctttcat-ttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
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-----------------------------------------------------------------------------------------------------------gtatatatattttgaacctagtcatc-atcctaaactcataaatgggcttggagctttgaagtatgaaaatggcttatgtacattgcagAATGAAGATGGTGGGTGGGGATTGCATATTGAGGGACACAGCACAATGTTTTGTACAACACTTAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCGCG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01290.t01 (Vitis vinifera), 3'ss of exon 3
gtatagttattcaattttaggatgcatttgtttaaccaagcataatgtagagatacaaaattgtaacattttcctcggtcaaatttcttgtatcttttaattaacttgttgtatttgcttaatcaggaagtttataatctattcattgcaacaataagtaattaatattatcccttttgttctttcatttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
| | | ||| ||| || | | | | | | | || | | || | || | | | | ||| | || | ||| ||||||||||||| || |||||| | || || ||||| || ||||| |||||||||||| | || ||||| || || ||| | || ||||||||||| |
-----------------------------------------------------------------------------------gtacatatat-tttgaacctagtcatcatcctaacctcataaatgggcttggag-ctttaaagtatgaaaatggcttatgtacattgc---------------------agAATGAAGATGGTGGGTGGGGATTTCATATTGAGGGACACAGCACCATGTTTTGTACAACCCTCAACTACATTTGTATGTGCATCCTTGGAGAAGGGCGAG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 3
gtatagttattcaattttaggatgcatttgtttaaccaagcataatgtagagatacaaaattgtaacattttcctcggtcaaatttcttgtatcttttaattaacttgttgtatttgcttaatcaggaagtttataatctattcattgcaacaataagtaattaatattatcccttttgttctttcatttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
| ||| |||| | | || || || | ||| | | |||| | ||| | | | || || || ||| ||| | || ||||||||||||| || |||||| | || || ||||| || ||||| |||||||||||| |||| | ||| || || ||||| || ||||||||||| ||
-------------------------------------------------------------------------------------gtatatatattttga--acctagtc--atcctcctaacc-------tcataaatgggt--ttggagcttcgaagtatgaaaatgg---cttatgtacatt-----gcagAATGAAGATGGTGGGTGGGGATTCCATATTGAGGGACACAGCACCATGTTTTGTACAACACTCAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCCCG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 3
gtatagttattcaattttaggatgcatttgtttaaccaagcataatgtagagatacaaaattgtaacattttcctcggtcaaatttcttgtatcttttaattaacttgttgtatttgcttaatcaggaagtttataatctattcattgcaacaataagtaattaatattatcccttttgttctttcatttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
| | | ||| ||| || | | | | | | | || | | || | || | | | | ||| | || || ||| ||||||||||||| || |||||| | || || ||||| || ||||| |||||||||||| | || | ||| || || ||||| || ||||||||||| |
-----------------------------------------------------------------------------------gtacatatat-tttgaacctagtcatcattctaacctcataaatgggcttggag-ctttaaagtatgaaaatggcttatgaacattgc---------------------agAATGAAGATGGTGGGTGGGGATTTCATATTGAGGGACAAAGCACCATGTTTTGTACAACCCTCAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCGAG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 3
gtatagttattcaattttaggatgcatttgtttaaccaagcataatgtagagatacaaaattgtaacattttcctcggtcaaatttcttgtatctttt-aattaacttgttgtatttgcttaatcaggaagtttataatctattcattgcaacaataagtaattaatattatcccttttgttctttcatttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
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-------------------------------------------------------------------------------------gtatatatattttgaacctagtcatcatcctaacctcataaatgggcttggag-ctttgaagtatgaaaatggcttatgtacatggc---------------------agAATGAAGATGGTGGGTGGGGATTGCATATTGAGGGACACAGCACAATGTTTTGTACAACACTCAGCTACATTTGTATGCGTATCCTTGGAGAAGGGCGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcattgcaacaataagtaattaatattatcccttttgttctttcatttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
aattaat putative branch site (score: 3)
ttatcccttttgttct CT-rich tract
attgcaacaataagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagttattcaattttaggatgcatttgtttaaccaagcataatgtagagatacaaaattgtaacattttcctcggtcaaatttcttgtatcttttaattaacttgttgtatttgcttaatcaggaagtttataatctattcattgcaacaataagtaattaatattatcccttttgttctttcatttaaagAATGAAGATGGAGGATGGGGACTACACATAGAGGGTCATAGCACTATGTTTTGTACAGCACTGAACTATATATGCATGCGAATTCTTGGAGAAGGACCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA