Sequence
atgc intronic sequence ATGC exonic sequencegtgaagctttgattatttctgttgcatactttgaatattcacttgtgctgatctggaaataaaaaaaaatggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
Basic information
species | Glycine max |
transcript | GLYMA15G25390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 3
--gtgaagctttgattatttctgttgcatactttgaatat---tcacttgtgctgatctggaaataaaaaaaaatgg-------------tgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
|| || | | ||| | | || ||| ||| | ||| | | | | | | || | || | || ||||||||||||| || |||||||||||||| ||||||||| || |||||||| | ||||| || ||||| ||||| ||||| |||||||||||||||||||
gtctgcagtcatcttgttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGAAGCTATGACTTAAACTTTAAGAATCAGCCTAATGATGGAGCTCATGTTC
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 3
--gtgaagc--tttgattatttctgttgcatactt---tgaatattcacttgtgctgatctggaaataaaaaaaaa----tggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
|||| | | | || || ||| |||| ||| | ||| |||| | || | ||| | |||| || | ||||||| ||||| || ||||||||||| || |||||||| || ||||||||||| |||||| | ||||| ||||| ||||| |||||||||| |||||||
gtgtgatatcatctaactagtttcattggccacttgtttgattgttctcttgattttattttgaattttaaaacaaatcctaatgcagATCAAAATTGGAATGGATGTTGCGGCATCAGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGTCCATGTTC
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 3
--gtgaagc--tttgattatttctgttgcatactt---tgaatattcacttgtgctgatctggaaat---aaaaaaaaat---ggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
|||| | | | || || ||| |||| ||| | || ||||| | || |||| ||| | |||| ||||||| ||||| |||||||||||||| || || ||||| || ||||||||||| |||||| | ||||| ||||| ||||| ||||||||||| ||| |||
gtgtgatatcatctaactagtttcattggccacttgtttgattgctctcttgttttttactttaaatgttaaacacaaatcctaatgcagATCAAAATTGGTATGGATGTTGCGGCATCTGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGCCCATATTC
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------gtgaagctttg-attatttctgttgc-----atactttgaatattcacttgtgctgatctggaa--------ataaaaaaaaatggt-gcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
| ||| | | || | |||| | | | || | ||| |||| | |||| | | ||| | |||||| |||||||| ||||||||||| || ||||| |||| || || ||||| | || |||||||||||||||||||||||||| ||||||||||| || |
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
upper sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
----gtgaagctttgattat-ttctgttgcatactttgaatattcacttgtgctgatctggaaataaaaaaaaatggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
| | ||| || | || | || | ||||| | | |||| | | | | ||| ||||| ||||||| |||||||| ||||||||||||||||||||||| | |||||| |||||||| ||||||||||| || |||||||| ||||||||||||||||| ||||
gtaggcgggttgttgcttttcttttcttttgcagtttgatt--ttccttgcagcctttaaggactccaaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatactttgaatattcacttgtgctgatctggaaataaaaaaaaatggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
tgctgat putative branch site (score: 3)
tggaaataaaaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagctttgattatttctgttgcatactttgaatattcacttgtgctgatctggaaataaaaaaaaatggtgcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA