Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggtttgttatttctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
Basic information
species | Glycine max |
transcript | GLYMA08G14050.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggttt---gttatt-tctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
||||| | || | ||| ||| | || | | | | | ||| ||| || | | |||||| | | | | | | ||||||||||| || |||||||| ||||| |||||||||||||| ||||||||| | ||||| |||||||||||||| || |||| || ||| ||| ||||
gtaaacataa-ctttactttg-ctctagctactccaatcttcctgaggctagcttgtttaaccattaactctctctggttattgtatatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA
upper sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggtttgttatttctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
||| ||| | || ||| | | | || || | | |||| ||||| | | | ||| | | | | | ||||||||||| ||||||||| | || || || ||||| ||| |||||| ||||| ||| | ||||||||||||||||| || ||| |||| || ||||||
gtaccaaa---cgct-ctttattctttatggtagaaaat--agtttggtgtgtttat-gactactgactcccttggcacctggaaata-tattagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
upper sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggtttgttatttctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
|||| ||| | || || | | | ||| || | || || | ||| ||||| | |||| | | ||| | ||||||||||| || |||||||| ||||| || || | ||||||||||| ||||| ||||| ||||||||||| || || ||||| || ||| | ||||||
gtaacaaaacaaacacttt---ttttttatctctcagtttccattgatctaaagctttaaa--taaaacgttttg--aatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
upper sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtaaaaaa--gttctctgcttaaattctcattgtgtc-----atttccagttaa-tattgtttgccaaacttaaaatggtttgttattt-ctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
| ||| | || | || | ||| | | || || || | | ||| || || | | || || ||| | ||| || |||||||||||||| || ||||| ||||| ||||||||||| |||||||||||||| || || ||||||||||| || || |||||| |||| |||||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
upper sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
-------------gtaaaaaa--gttctctgcttaaattctcattgtgtc-----atttccagttaa-tattgtttgccaaacttaaaatggtttgttattt-ctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
| ||| | || | || | ||| | | || || || | | ||| || || | | || || ||| | ||| || |||||||||||||| |||||||| ||||| ||||||||||| |||||||||||||| || || ||||||||||| || || |||||| |||| |||||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttaatattgtttgccaaacttaaaatggtttgttatttctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
agttaat putative branch site (score: 4)
tttgttatttcttttt putative PPT
tttgttatttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggtttgttatttctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA