Sequence
atgc intronic sequence ATGC exonic sequence...cactatttcagtctttcgctttggagtttggataatgtctttatgagtgtatgtttgtaatcacaacatcttagtgaccaaatttgtcaatctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCTCAAGAGAACTATCATATCTGCCCATATCCAGATTGTGGAAAGAGATATGCTC
Basic information
species | Glycine max |
transcript | GLYMA08G13310.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G06634.1 (Arabidopsis thaliana), 3'ss of exon 4
--cact-atttcagtctttcgctttgg---agtttggataatgtct--ttatgagtgtatgttt-gtaatcacaacatcttagtgaccaaatttgtcaatctgc---tgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCTCAAGAGAACTATCATATCTGCCCATATCCAGATTGTGGAAAGAGATATGCTC
| | |||| || || | | | ||||| | ||| | ||| | || | | || | | | || ||| | | || ||||||| ||||| ||||||| ||| | |||||||||||||| || ||||| |||||||| |||||||| || || || | |||| |||||||||||||
gtgattgattttgatcactctcactagcttagtttatttggtgtataattaggcaattaggcaaagggattgtgttgcgtgttttagtaactttctgtagttgtggatgcagGCATTCTCGTTGGATTTTAACCTTAGGTCTCACATGAAGACTCATTCACAAGAGAATTATCATATATGTCCTTACAGTGGGTGTGTGAAGAGATATGCTC
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 4
--cact-atttcagtctttcgctttgg---agtttggataatgtct--ttatgagtgtatgttt-gtaatcacaacatcttagtgaccaaatttgtcaatctgc---tgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCTCAAGAGAACTATCATATCTGCCCATATCCAGATTGTGGAAAGAGATATGCTC
| | |||| || || | | | ||||| | ||| | ||| | || | | || | | | || ||| | | || ||||||| ||||| ||||||| ||| | |||||||||||||| || ||||| |||||||| |||||||| || || || | |||| |
gtgattgattttgatcactctcactagcttagtttatttggtgtataattaggcaattaggcaaagggattgtgttgcgtgttttagtaactttctgtagTTGTGGATGCAGGCATTCTCGTTGGATTTTAACCTTAGGTCTCACATGAAGACTCATTCACAAGAGAATTATCATATATGTCCTTACAGTGGGTGTGTGA------------
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 4
cactatttcagtctttcgc--tttggagtttggataatgtctttatgagtgtatgtttgtaatcacaacatct---tagtgaccaaatttgtcaatctgc-tgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCTCAAGAGAACTATCATATCTGCCCATATCCAGATTGTGGAAAGAGATATGCTC
| || | | |||| | | | || | | | | | ||||| | | | | | || ||||| || || ||||||| ||||| || |||||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||||||||||||||
---caggccaattctagatcatttgatatct---ttattcttgcgcaaaacttttcctttaatctctatgtgtgcattgtaaccaatttcacacataaaaatgcagGCATTCTCTCTAGATTTCAATTTAAGGTCACACATGAAAACACATTCACAAGAGAACTACCATATCTGCCCCTATCCAGATTGTGGAAAGAGATATGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgtatgtttgtaatcacaacatcttagtgaccaaatttgtcaatctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCTCAAGAGAACTATCATATCTGCCCATATCCAGATTGTGGAAAGAGATATGCTC
tttgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cactatttcagtctttcgctttggagtttggataatgtctttatgagtgtatgtttgtaatcacaacatcttagtgaccaaatttgtcaatctgctgcagGCCTTCTCCCTGGATTTCAACTTAAGGTCTCACATGAAAACACATTCTCAAGAGAACTATCATATCTGCCCATATCCAGATTGTGGAAAGAGATATGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - -gctttgg
- - - - - - - - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaatt