Sequence
atgc intronic sequence ATGC exonic sequence...attgtgtttcatgctatatatgatattatcttataaatatgtttattgataaagaaaaatgatcattatttttgcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
Basic information
species | Glycine max |
transcript | GLYMA02G05160.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
----------attgtgtttcatgctatatatgatatta---tcttataaatatgtttat-tgataaa-gaaaaatgatcattattt-ttgcatctctt---cac-tttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
|| | | | | || | | |||||| || | | | | || || | ||| | ||| |||| || | | | | || || ||| | | || |||||||||| || ||||||||||| || || || |||||||||||||| ||||||||||| || ||||| ||||| ||||| ||||| |
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------------attgtgtttcatg-ctatatatgatattatcttataaatatgtttattgataaagaaaaat----gatcattattt----ttgcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
| | || | ||| |||| || |||| | | ||| | | || | | || | || | | ||| |||| | | || | ||||| |||||||||| || ||||||||||| || || ||||||||||||||||| |||||||||||||| ||||| || ||||||| || || |
gtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatga-atcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaa-cagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAATGGAGCCACTGTGAATCTTGGGCTATGGGATACCGCAG
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
attgtgtttcatgctatatatgatattatcttataaatatgtttattgataaagaaaaatgatcattatttttgcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
||| | | | ||| | | || || | | ||| | | || || | ||| | | || ||||| | | ||||||||||||| || |||||||| |||||||| || ||||| || || |||||| |||||| ||||| ||||| ||||||||||| |
-----gttatgtcccaattattctttcatgtttcttgtttcattaccacaacaacaacatatctcatgtttct-----tgtttcttttgtggatatacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
--attgtgtttcatgctatatatgatattatcttataaatatgtttattgataaagaaaaatgatcattatttttgcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
| | | | | | | | || || | | | ||| || | | | | ||||| || || | | | || || ||||| |||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || || ||||| ||||| |
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatttttgaa--ttattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
upper sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 2
attgtgtttcatgctatatatgatattatcttataaatatgtttattgataaagaaaaatgatcatt------atttttgcatctctt-cactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
| | || | | | | | ||| | || || || | |||||| | | | | || || ||||||| || ||||| || || |||||||||||||||||||| || || ||||| ||| || ||||| ||||||||||| || || |
-------ggcgtactgcaaggagatgtgttgtgcgatgtctcccattcactaaagtctctggtcccttcaacgatttttaaagcacagataattggtcgttttgcagGATTACGTACCAACCGTGTTTGACAATTTCAGCGCAAATGTCGTGGTCGATGGAAACACAGTCAATCTCGGATTATGGGATACAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgataaagaaaaatgatcattatttttgcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
tattgat putative branch site (score: 3)
tctcttcactttgttt putative PPT
aaagaaaaatgatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgtgtttcatgctatatatgatattatcttataaatatgtttattgataaagaaaaatgatcattatttttgcatctcttcactttgtttggaaatagGATTATGTGCCAACTGTTTTCGACAATTTCAGCGCAAATGTGGTTGTGAATGGAGCCACTGTTAATCTAGGATTATGGGACACTGCCG
- - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa