Sequence
atgc intronic sequence ATGC exonic sequencegtgggtgaagttttgattatttctgttgcataatttgaatattcacttgtgctgatctggaaataaaaaacaatggtgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
Basic information
species | Glycine max |
transcript | GLYMA04G24920.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 3
gtgggtgaagttttgattatttctgttgcataatttgaatat---tcacttgtgctgatctggaaa--taaaaaacaatgg-----------tgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
| || ||| | | ||| | | || ||| ||| | ||| | | | | | | || || || || || |||||||||||||||| |||||||||||||| ||||||||| || |||||||| | ||||| || ||||| | ||| ||||| |||||||||||||||||||
--gtctgcagtcatcttgttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGAAGCTATGACTTAAACTTTAAGAATCAGCCTAATGATGGAGCTCATGTTC
upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 3
gtgggtgaagttttgattatttctgttgcata---atttgaatattcacttgtgctgatctggaaataaaaaacaa----tggtgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
||| | | | | | || || ||| | ||||| | ||| |||| | || | ||| | ||||||| | ||||||| |||||||| ||||||||||| || |||||||| || ||||||||||| |||||| | ||||| | ||| ||||| |||||||||| |||||||
gtgtgatatcatctaactagtttcattggccacttgtttgattgttctcttgattttattttgaattttaaaacaaatcctaatgcagATCAAAATTGGAATGGATGTTGCGGCATCAGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGTCCATGTTC
upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 3
gtgggtgaagttttgattatttctgttgcata---atttgaatattcacttgtgct--gatctggaaataaaaaacaa----tggtgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
||| | | | | | || || ||| | ||||| | || ||||| | | | | | ||| |||| | ||||||| |||||||||||||||||||| || || ||||| || ||||||||||| |||||| | ||||| | ||| ||||| ||||||||||| ||| |||
gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC
upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------gtgggtgaagttttg-attatttctgttgc-----ataatttgaatattcacttgtgctgatctggaa--------ataaaaaacaatggt-gcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
| | | ||||| | || | |||| | | || || | ||| |||| | |||| | | ||| | |||||| ||||| || ||||||||||| || ||||| |||| || || ||||| | || ||||||||||||| |||||||||||| ||||||||||| || |
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
gtgggtgaagttttgattat-ttctgttgcataatttgaatattcacttgtgctgatctggaaataaaaaacaatggtgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
|| || | | ||| || | || | || | ||||| | | |||| | | | | ||| |||| ||||||| ||||| || ||||||||||||||||||||||| | |||||| |||||||| ||||||||||| || | |||||| ||||||||||||||||| ||||
gtaggcgggttgttgcttttcttttcttttgcagtttgatt--ttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcataatttgaatattcacttgtgctgatctggaaataaaaaacaatggtgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
tgctgat putative branch site (score: 3)
aaataaaaaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtgaagttttgattatttctgttgcataatttgaatattcacttgtgctgatctggaaataaaaaacaatggtgcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA