Sequence
atgc intronic sequence ATGC exonic sequencegttagataatccactgatctttgatctgaatgaacttgattcttggagtcatggtcgtattctgattatctcttttgtttctaagtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGTAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTATTCAAAGGAGGCACCAAAAG
Basic information
species | Glycine max |
transcript | GLYMA04G11550.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 6
gttagataatccactgatctttgatctgaa----tgaacttg-attct------tggagtcatg-gtcgtattctgattatctcttttgtttctaa--gtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGTAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTATTCAAAGGAGGCACCAAAAG
|| | | | | || ||| | || | || | ||| ||| || ||||||| | |||| |||| | | || || | |||||| || ||||| ||||| ||||| ||||||||||| || |||||||| ||||| | || || |||||||||||| | ||| || | ||||| |||
-atactttacacctttattttttagatggaagcctggaattgtgctctgttatctgtagtcatgcattatatt-tgatcttaaatcttattctctattgtagAGTCGGCATCTTGAAGTTCAGTTGCTTTGTGATCAATATGGTAATGTAGCAGCACTTCACAGTCGTGATTGCAGTGTGCAACGGCGACACCAGAAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 5
--gttagataatccactg-atcttt-gatctgaatgaacttgattcttggagtcatggtcgtattctgattatctcttttgtttctaagtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGTAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTATTCAAAGGAGGCACCAAAAG
| | || | ||| |||||| ||||| ||| | ||||| | | || || | | | || | | | | |||||| |||||| |||| | |||||| |||||||| || || || || || ||||||||||||||||||||||| || | || || || |||||||||
gtaatggctacttaactatatcttttgatctcaatataactgatt------aacttagtaatacgtgggatgttctttatatat-tgtgtagAGTCGACATTTAGAGGCCCAGTTGCTTTGTGACCAATATGGAAACGTAGCAGCTTTGCATAGCCGTGATTGTAGCGTCCAGAGAAGACACCAAAAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G36180.2 (Arabidopsis thaliana), 3'ss of exon 5
--gttagataatccactg-atcttt-gatctgaatgaacttgattcttggagtcatggtcgtattctgattatctcttttgtttctaagtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGTAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTATTCAAAGGAGGCACCAAAAG----
| | || | ||| |||||| ||||| ||| | ||||| | | || || | | | || | | | | |||||| |||||| |||| | |||||| |||||||| || || || || || ||||||||||||||||||||||| || | || || || |||||||||
gtaatggctacttaactatatcttttgatctcaatataactgatt------aacttagtaatacgtgggatgttctttatatat-tgtgtagAGTCGACATTTAGAGGCCCAGTTGCTTTGTGACCAATATGGAAACGTAGCAGCTTTGCATAGCCGTGATTGTAGCGTCCAGAGAAGACACCAAAAGGTAT
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
gttagataatccactgatctttgatctgaatg---aactt-----------gattcttggagtcatggtcgtattctgattatctcttttgtttct---aagtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGTAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTATTCAAAGGAGGCACCAAAAG
|| | || ||| |||| || |||| |||||| | | | || |||||| || |||||||| || ||| |||||| || ||||| || ||| ||||||| |||||||| ||||||||| | || ||||| ||||| |||||||||||||||||||| |||||||| | || ||||||
gtgatattatctactgcgctctgatttgaatgctgagccttttagatttccagttgctggagtttacttcttattctgacaattcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgattcttggagtcatggtcgtattctgattatctcttttgtttctaagtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGTAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTATTCAAAGGAGGCACCAAAAG
ttctgat putative branch site (score: 3)
ttatctcttttgtttc CT-rich tract
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagataatccactgatctttgatctgaatgaacttgattcttggagtcatggtcgtattctgattatctcttttgtttctaagtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGTAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTATTCAAAGGAGGCACCAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG