Sequence
atgc intronic sequence ATGC exonic sequence...ttctctcacatacataccaaatatatgcatttaaatatgtcttttttattcattgcaacttttacttcaattatataaatattcattctgatttgtccagTGGATGGTGGATGAGAATGAACTCCGTGTAATTCATTATACACTAGGTCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
Basic information
species | Glycine max |
transcript | GLYMA10G30700.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30700.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 3'ss of exon 4
ttctctcacatacataccaaatatatgcatttaaatatgtcttttt-tattcattgcaacttttacttcaattatataaatattcattctgatttg--tccagTGGATGGTGGATGAGAATGAACTCCGTGTAATTCATTATACACTAGGTCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
| ||| || | | | | | | || |||| || | | ||| || | | | | || || | | | | || | || | ||||||||||| |||||||| ||||| | || ||||| || ||||| || ||||||||||| |||||||||||||| |||||||||| |||||||| | |
---tttcagatttagaacgttttaacaccttatgatatctcatcatatataatccacagcctgctgattatttgtaaacgtcgccttcctaactttgctgcagTGGATGGTTGATGAGAAAGAACTTAGGGTCATTCACTACACACTTGGGCCTCTTAAGCCCTGGGACTGGTGGACTGCTTGGCTTGTTAAACCTGTGGCAG
upper sequence: GLYMA10G30700.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 3
-----ttctctcacatacataccaaatatatgcatttaaatatgtcttttttattcattgcaacttttacttcaattatataaatattcattctgatttgtccagTGGATGGTGGATGAGAATGAACTCCGTGTAATTCATTATACACTAGGTCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
| | | | | || |||||| | | | | || | || || || | | | | | | ||||| |||| | ||||||||||| ||||| | | |||| | || ||||| || || ||||| ||||||||||||||||||||||||||| | ||||| ||||||||||||||||
acgtagtggttaatttgggattggttttgattggtttaaaagtataactgtctttttcttcagctgtt--tgaatctttgtgttttctcatt---atttctgcagTGGATGGTTGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATG
upper sequence: GLYMA10G30700.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 4
------ttctctcacatacataccaaatatatgcatttaaatatgtcttttttattcattgcaacttttacttcaattatataaatattcat-tctgatttgtccagTGGATGGTGGATGAGAATGAACTCCGTGTAATTCATTATACACTAGGTCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
|| | | | | |||| | | | | | | | | |||| || | | || | || || | || | | ||||||||||| ||||| | |||||||||| || || || ||||| || || ||||| || ||||| |||||||| ||||||||| | |||||||||||||
caagaaatccttagtaggactgaggcctgcatgcttctgattgttttaaatctgccaattggaaaaaaaattctcatc-------tgtttatgtgtggtaaatgcagTGGATGGTAGATGAAGAAAAACTCCGTGTTATCCACTACACACTTGGCCCCCTTAAACCATGGGATTGGTGGACGTCTTGGCTTCTAAAACCTGTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattcattgcaacttttacttcaattatataaatattcattctgatttgtccagTGGATGGTGGATGAGAATGAACTCCGTGTAATTCATTATACACTAGGTCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
ttctgat putative branch site (score: 3)
tttgtcc CT-rich tract
ttttacttcaattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctctcacatacataccaaatatatgcatttaaatatgtcttttttattcattgcaacttttacttcaattatataaatattcattctgatttgtccagTGGATGGTGGATGAGAATGAACTCCGTGTAATTCATTATACACTAGGTCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - cacatac
- - - - - - - - ccaaata
- - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctg