Sequence
atgc intronic sequence ATGC exonic sequencegtaacaaaataagcaggacttgctctcatttttaaaatgaatattgtcttgttatattcattgattactttttatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
Basic information
species | Glycine max |
transcript | GLYMA10G32480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 4
gtaacaaaataagcaggacttgctctcatttttaaaatgaatattgtcttgttatattcattgattactttttatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
||| |||| | | ||| || ||| | || || | ||| | | | || | || || |||| |||||||||||||| ||||| ||| |||||||||||||||| ||||| |||||||| || || |||||||| || |||||||||||||| || ||||
gtatttaaattccttcaagtggctttcgtttgacatttgtttagttggttgatgtgaatgtggaatctgatt--------ttcagGTGGAACATGTAAAAGCAGAGAGAAATTTACTTGCAGAAGTTGATAGCAATTGCATTGTCAAACTGTATTGTTCTTTCCAAGATGAAGAGTACTTGTATC
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaacaaaataagcaggacttgctctcatttttaaaatgaatattgtcttgttatattcattgattactttttatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
||| | | | | || | | || | | || |||| || | | || || |||| | | || | | || |||| || ||||| ||||| ||||| ||| |||||||||| ||||||||||| |||||||| ||||| |||||||| |||||||||||||||||||| ||||
gtatctccttcaagctgcttttgtttgatatatctt-tgtttattatcgt-tcatgtttgttgaaa---tctgattctttttcagGTGGAGCATGTGAAAGCAGAGAGAAATTTACTTGCAGAGGTTGACAGCAATTGCATTGTGAAGCTGTATTGTTCTTTTCAAGATGAAGAGTATTTGTATC
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 3
gtaacaaaataagcaggacttgctctcatttttaaaatgaatattgt-cttgttatattcattgattactttttatccc--tgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
||| | | | || || || || ||| | || | || | || || | | |||| ||| || | |||||||||||||||| || |||||||||||| |||||||||| ||||| ||||| |||||||| || ||||||||||| || ||||||||||||| | | ||||
gta-tgacttctgttggcctggcagacaattt---attgtgtgttatatttatttttcttattgcccgatttgcttcttaatatttagGTTGAACATGTGAAGGCTGAGAGGAATTTACTTGCAGAGGTTGATAGCAATTGCATTGTCAAACTTTATTGTTCATTCCAAGATGAAGAGTTTCTTTATC
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------------------------------gtaacaaaataagcagg-acttgctctcatttttaaaat-----gaatattgtcttgttatattcattgattactttttatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
|| || | ||| || | | | |||| | ||| || || || || || | | || |||| || |||||||| || ||||| ||| | |||||||| |||||||| |||||||| || ||| | ||||| ||||||||||| || |||| || ||
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgc--agGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 3
---gtaacaaaataagcaggacttgctctcatttttaaaatgaatattgt---cttgttatattcattgat-tactttttatcc--------ctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
| || | | || ||| | || | ||| || || | | || | |||| | | || |||| || ||||| ||||| ||||| |||||||| || ||||||||||||||||| ||||| ||| | |||||||| |||||||| || || || || ||
ccgttgttttcatgcttgatatgcatacaagttcttagggagtttaccttatccttcttgtacttaaccatgtgctttcaacgcaacgtggtcttggcagGTAGAGCATGTTAAAGCAGAGAGAAATCTACTCGCTGAAGTTGACAGCAACTGTATTGTGAAGTTGTATTGTTCATTTCAAGACGAGGATTACTTGTACT
upper sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------gtaacaaaataagcaggacttgctctcatttttaaaatgaatattgtcttgttatattcattgatt---actttttatccctgtt-tagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
| | || | | | | | | || | | ||| || | ||| |||||| | | |||| || |||| || ||||||||||| ||||| ||| | |||||||| || || ||||| || ||||| ||| | ||||| || ||||||||||| |||||||| |||
tcatcataagaatgataacaataataatgataaatatttttatcgactatgatagtgaaaaatcatagccattgaattgaaaattttgcggtaattgcagGTGGAGCATGTAAAAGCAGAGAGAAATTTGCTTGCAGAGGTCGATAGCAATTGTATTGTGAAGTTGTATTGCTCGTTTCAAGATGAGGAGTATTTGTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaaatgaatattgtcttgttatattcattgattactttttatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
cattgat putative branch site (score: 4)
ctttttatccctgttt putative PPT
ttgttatattcattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaaaataagcaggacttgctctcatttttaaaatgaatattgtcttgttatattcattgattactttttatccctgtttagGTTGAACATGTAAAAGCTGAGAGGAATCTACTTGCAGAAGTTGACAGCAACTGCATTGTAAAGCTTTATTGTTCCTTTCAAGATGAAGAGTATTTATATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA