Sequence
atgc intronic sequence ATGC exonic sequencegtggagcttcctataagatcttgttctgccttagctttgatcatctctgtagtaagaaataaactgaagctctgaactgtatttttatagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
Basic information
species | Glycine max |
transcript | GLYMA07G08030.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 5
gtggagcttcctataagatcttgttctgccttagctttgatcatctctg-tagtaagaaataaactgaagctctgaactgtatttttatagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
|| | || | | |||| || || | | | | ||| | |||| | | | | | |||| ||||| |||||||| || ||||||||||| ||||||||||| |||||||||||||||
------------gtagaaactgagtttcttttagattctttccttaatcctcatgcaggatatatc--agcttaccattttttacctgcagCTTTCTGTGGAAAGGCTAAGCTCAATGAAGAAGTATGTCTTTGGGTTAGGCTCTGCTCAG
upper sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 5
gtggagcttcctataagatcttgttctgccttagctttgatcatctctgtagtaagaaataaactgaagctctgaactgtatttttatagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
|| || |||| | || | || ||||| | | | | ||| | | | | | || | ||| | |||| ||||||||||| || ||||| |||||||||||||| |||||||||||||| ||||||
gtattatttgatatatgtgtatgctacctttttgcttttgaactgtgtttggtagaa---gagccaatattttgtttatttctttgacagCTATCTGTTGAAAGACTGAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCAGCTCAG
upper sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 4
-----gtggagcttcctata-agatcttgttctgccttagctttgatcatctctgtagtaagaaataaactgaagc-tctgaactgtattttt---atagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
| || | ||| | || |||||| || ||||||| || | |||| || | | || | | | | ||||| | | |||||||||| |||||||||||||| |||||||||||||| |||||||||||||| || |||
gttaacttcagtatttgatatatatgttgttcctttttc-ctttgat-atgtgcttagtggaaagaagagccaattatttcgattctatttgtctgacagCTCTCTGTCGAAAGGCTTAGTTCCATGAAGAAATATGTTTTTGGATTAGGCTCCGCGCAG
upper sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 3
gtggagcttcctataagatcttgttctgccttagctt---------------tgatcatctctgtag-----taagaaataaactgaagctctgaactgtatttttatagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
||||| || | || || | | |||| || || |||| ||| | || ||| ||| ||| |||| || ||| | || |||| |||||||||||||| ||||| |||||||||||||| |||||||| ||| ||||||||
gtgga-ctccataaaatctttatttctttttttatttgttaatctaagacaatgatgttctttataaatgaataaaaaaaaaattgaaccttctgtctgca---ttgcagCTATCTGTTGAAAGGCTGAGTTCCATGAAGAAATATGTTTTTGGATTGGGCACTGCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatcatctctgtagtaagaaataaactgaagctctgaactgtatttttatagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
ctttgat putative branch site (score: 5)
tattttt putative PPT
aactgtatttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggagcttcctataagatcttgttctgccttagctttgatcatctctgtagtaagaaataaactgaagctctgaactgtatttttatagCTCTCTGTTGAAAGGCTTAGTTCAATGAAGAAATATGTCTTTGGATTAGGCTCTGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA