Sequence
atgc intronic sequence ATGC exonic sequence...ccctggataccaaatatatatttgtctctgagcattcatttgtattgcatctttcgattctattatctaacattcaaactattcgtgctgatcaatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
Basic information
species | Glycine max |
transcript | GLYMA19G43630.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 3'ss of exon 4
ccctggataccaaatatatatttgtctctgagcattcatttgtattgcatctttcgattctattatctaacattcaaactattcgtgctga--tcaatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
||| || | | || || | ||| ||| | || | || | || | | | || | | | ||||||||||| |||||||| ||||| | || |||||||| ||||| || || |||||||| |||||||||||||| |||||||| | |||||||| | |
tttcagatttagaacgttttaacaccttatgatatctcatcatatataatccacag--cctgctgattatttgtaaacgtcgccttcctaactttgctgcagTGGATGGTTGATGAGAAAGAACTTAGGGTCATTCACTACACACTTGGGCCTCTTAAGCCCTGGGACTGGTGGACTGCTTGGCTTGTTAAACCTGTGGCAG
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 3
ccctggataccaaatatatatttgtctctgagcattcatttgtattgc-atctttcgattctattatctaacattcaaactattcgtgctgatcaatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
| | | || | ||| || | || | |||| | ||||| ||| | | | | | | ||| | || | ||||||||||| ||||| | | |||| | || |||||||| || || ||||| ||||||||||||||||||||||| | ||||| |||||||||||||||
acgtagtggttaatttgggattggttttgattggtttaaaagtataactgtctttttcttcagctgtttgaatctttgtgttttctcatt-atttctgcagTGGATGGTTGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATG
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 4
ccctggataccaaatatatatttg-tctctgagcattcatttgtattgcatctttcgattctattatctaacattcaaactattcgtgc-tgatcaatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
| || | | || | | || || | |||| || |||| | ||| | | || | | || || || || | ||| ||||||||||||||||| | |||||||||| || ||||| ||||| ||||||||||| || ||||| |||||||||||||||||| | |||||||||||||
caagaaatccttagtaggactgaggcctgcatgcttctgattgttttaaatctgccaattggaaaaa--aaattctcatctgtttatgtgtggtaaatgcagTGGATGGTAGATGAAGAAAAACTCCGTGTTATCCACTACACACTTGGCCCCCTTAAACCATGGGATTGGTGGACGTCTTGGCTTCTAAAACCTGTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatctttcgattctattatctaacattcaaactattcgtgctgatcaatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
attctattatctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccctggataccaaatatatatttgtctctgagcattcatttgtattgcatctttcgattctattatctaacattcaaactattcgtgctgatcaatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
ccctgga
- - - - -ccaaata
- - - - - - - - - - - -gtctctg
- - - - - - - - - - - - - - - -gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcgtgc