Sequence
atgc intronic sequence ATGC exonic sequence...gttcttgtagaccaaaaattattgtattagacatatgtctatgttggatgatattatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG
Basic information
species | Glycine max |
transcript | GLYMA08G17400.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G17400.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g07770.1 (Oryza sativa), 3'ss of exon 1
----gttcttgtagaccaaaaattattgtattagacatatgtctatgttggatgatattatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG
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gtacgcatcatcaatctctcaatcaattctctccaaaaaaatcgaaacaaga-attaatctcttctttcttacgatgaattgatgatcgtctt-gtcgtcgcagAGGCGACGCCCAAGACGATCATGAGGGTGATGGGAGTGAAGGGCCTCACCCTCTACCACCTCAAGAGCCATCTCCAG
upper sequence: GLYMA08G17400.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------------------gttcttgtagaccaaaaattattgtattagaca--tatgtctatgttggatgatattatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG
|||||| | | || | | | | || | | || | || || | | | || || || ||| ||| | | ||| |||||| ||||| || || ||||||||||||||||| || ||||| ||||| |||||||| ||||||||||| || |||
gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattacttgtatgtttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatc----aattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
upper sequence: GLYMA08G17400.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G081671_T01 (Zea mays), 3'ss of exon 1
---------------------gttcttgtagac-caaaaattattg-tattagacatatgtctatgttggatgatattatgatctt--ttgattaatcatctttttct---cttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG
| ||| || | | | ||| || | | | || || ||||| | || || |||||| |||| || || | || | | |||||| || || || |||||||||||||||||||| || ||||| |||||||| |||||||||||||| ||||| |||
gtacgtgatacatagagatgcatgctttcagttacgttacgtgttgctacttgccgctgtggaattttatttgatacgttaattttggttgatttg-catccttccctaaattcttcgccgtacgtagAGGCAACGCCCAAGACCATCATGAGGGTTATGGGAGTCAAGGGCCTCACCCTCTACCACCTCAAGAGTCACCTTCAG
upper sequence: GLYMA08G17400.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G052544_T01 (Zea mays), 3'ss of exon 1
gttcttgtag-accaaaaattattgtattagaca-tatgtctatgttggatgatattatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG
|| | ||||| | | | || ||| | ||| | |||| | ||| | || || |||||| |||||||| ||||| || |||||||||||||| ||||| || ||||| || ||||| ||||||||||||||||| || |||
gtacgtgtagtagtagctactagctagctagctgctgctagctccctggcccggtcgctcgtcttggttctgatcgt-ttcctccctttttctctcacgcagAGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAG
upper sequence: GLYMA08G17400.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S201_75V6.1 (Physcomitrella patens), 3'ss of exon 1
-gttcttgtagaccaaaaattattgtattagacatatgtctatgttggatgatattatgatcttttgattaatcatctttttctcttttt-tggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG
| ||| | | | | || || | | | | | |||| | | | || | | || | | | | | | | | | ||||||| || || || | | |||||||||||||| ||||||||||| || || ||||| | |||||||| ||||||
tgggcttct-gctgagagatgatcggagtgtaggtg-atctaaacgattcgtagtgacgaagtccaactctctcgtttgtctgtggtgaaatcaactgacagAGGCTACACCGAAGTCTGTGATGAGGGTTATGGGAGTGAAGGGTCTTACGCTCTACCATTTGAAGAGCCATCTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatgatattatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG
gattaat putative branch site (score: 3)
tctttttctctttttt putative PPT
atattatgatcttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttgtagaccaaaaattattgtattagacatatgtctatgttggatgatattatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG
gttcttg
- - - - - accaaaa
- - - - - - - - - - - - - - - - - - gtctatg
- - - - - - - - - - - - - - - - - - - - - - tggatga