Sequence
atgc intronic sequence ATGC exonic sequence...gccactttttaagagccatgtggattgtcgggctcttcatagatgccaaaacttgacctaattcaaagttatctgttgtgtcttctgtgcatgtccacagGTTATTGGGTTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTGTTGAATCCCTCGATACTGCACGTGAAAGGGCAGAGGCTCGTGCTGAGTCAT
Basic information
species | Glycine max |
transcript | GLYMA08G18580.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G18580.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g49970.2 (Oryza sativa), 3'ss of exon 8
gccactt-tttaagagccatgtggattgtcgggctcttcatagatgccaaaacttgacctaattcaaagttatctgttgtgtcttctgtgcatgtccacagGTTATTGGGTTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTGTTGAATCCCTCGATACTGCACGTGAAAGGGCAGAGGCTCGTGCTGAGTCAT
||| || || || |||| | | | |||||| | | | || ||| || | | | | | | |||||||||||| ||||||||||| || |||||||||||||||||||| ||| || ||| ||| |||||||||||||||| | || |||||||| ||
gccttttactttagtaccattgagcattaaatgttcttcaaaagtttgtagtattattgtaagcatcctgaatttatcaagaaatg-atatgttatgacagGTTATTGGCTTGAATAATGTACCCCTTGCTGGTGATGAATTTGAGTCTGTGGACAACCTTGATGTTGCACGTGAAAGGGCAAACGCACGTGCTGAAGCAC
upper sequence: GLYMA08G18580.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G007038_T01 (Zea mays), 3'ss of exon 8
gccactttttaagagccatgtggattgtc--gggctcttcatagatgc-caaaacttgacctaattcaaagttatctgttgtgtcttctgtgcatgtccacagGTTATTGGGTTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTGTTGAATCCCTCGATACTGCACGTGAAAGGGCAGAGGCTCGTGCTGAGTCAT
|| | ||| || |||| | | | | || || | | ||| || | | | | |||||||||||| | ||||| ||||| |||| ||||||||||||||||||||||| ||| ||| ||||||||||||||| | | |||||||| ||
---acctccgaaggatgattccttttgttttaaccagtggttgaacgctcatggaacagcagtgatataagcatcctaactttttaagaaaaattctttacagGTTATTGGCCTCAATAACGTTCCCCTTGCCGGTGATGAATTTGAGGTTGTTGACAACCTTGATGTTGCACGTGAAAGGGCGAATGGGCGTGCTGAAGCAC
upper sequence: GLYMA08G18580.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------gccactttttaagagc--catgtggattgtc--------gggctcttcatag-atgccaaaacttg-acctaattcaaagttatctgttgtgtcttctgtgcatgtccacagGTTATTGGGTTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTGTTGAATCCCTCGATACTGCACGTGAAAGGGCAGAGGCTCGTGCTGAGTCAT
| || | | | | ||||| ||| || || | || ||| ||| | | | | ||| | | | | ||| | | | | ||||| ||||| || |||||||| || ||||||||||||||||||||| | || ||||| ||| || || || | ||||||||| ||||| | |||
gtttgtagtttcataatctaccctaagttaaacgtcattgcacacaaacgtcattgcaaacgtcattgcacacaaacgtcatgtttattttcttggtgacaggattttgatactatgttctcatgtatagatgatttagatatctaatttgaggatctaaaatacatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATCAC
upper sequence: GLYMA08G18580.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0027g00130.t01 (Vitis vinifera), 3'ss of exon 8
-gccactttttaagagcca-tgtggattgtcgggctcttcatagatgccaaaact-tgacctaattcaaagttatctgttgtgtcttctgtgcatgtccacagGTTATTGGGTTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTGTTGAATCCCTCGATACTGCACGTGAAAGGGCAGAGGCTCGTGCTGAGTCAT
| | ||| ||| ||| | || | | | | ||| ||| | ||| | | ||||||| | |||| ||||| |||||||||||||||||||||||||||||||||||||| |||| ||||| |||| ||| || ||||| || ||||| ||||| |||||||
gaaaatgtactaaatatggctgttatttgcatgatcatttgctgcttctgtgatagtgatctact---gtgttcttctaaatttcttctgaatgctgctgtagGTCATTGGATTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTCGTTGGCTCCCTTGATATTGCTCGAGAAAGAGCGGAGGCACGTGCAGAGTCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaaaacttgacctaattcaaagttatctgttgtgtcttctgtgcatgtccacagGTTATTGGGTTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTGTTGAATCCCTCGATACTGCACGTGAAAGGGCAGAGGCTCGTGCTGAGTCAT
acctaat putative branch site (score: 3)
taattcaaagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccactttttaagagccatgtggattgtcgggctcttcatagatgccaaaacttgacctaattcaaagttatctgttgtgtcttctgtgcatgtccacagGTTATTGGGTTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTGTTGAATCCCTCGATACTGCACGTGAAAGGGCAGAGGCTCGTGCTGAGTCAT
gccactt
- - - - - - - -ccatgtg
- - - - - - - - - - - - - - - - ctcttca
- - - - - - - - - - - - - - - - - - - - - - -ccaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg