Sequence
atgc intronic sequence ATGC exonic sequence...ccagtgttgtgttttgtttttttctggtggttattatgtgtagctgttttgtttgatgattgattgactcaaccaccttttgtgatgcaattaattgcagCTTCCTCCTGAATGGACAGACCAGTTTGAGTCAGGCATTCAG
Basic information
species | Glycine max |
transcript | GLYMA13G34980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 4
-ccagtgttgtgttttgtttttttctggtggttattatgtgtagctgttttgtttgatgattgattgactcaaccaccttttgtgatgcaattaattgcagCTTCCTCCTGAATGGACAGACCAGTTTGAGTCAGGCATTCAG
|| || | || |||| | | | ||| ||||| ||| | |||| | | || | ||| | |||| ||||||||||||||| |||||||| ||||| || || ||||||||||||
gtacgttttcaatcttaaattttattttttg--gttagatgtagaaatttatgatcctgat-ggctacctta--cacttaaaagtcaaaaatttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
upper sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------------------------------------------ccagtgttgtgttttgtttttttctggtggttattatgtgtagctgttttgt-ttgatgattgattgactcaaccaccttttgtgatgcaattaattgcagCTTCCTCCTGAATGGACAGACCAGTTTGAGTCAGGCATTCAG
| | | | | || || || | | | || ||| || || | | || ||||||||| || | ||||| | | ||||||||||||||||||||||||||||| || |||||||||||||||||||||
gtaagtaggagaacctcaaacacaaacgttctcttttgattgggtatttgataaaactaattaccattgtgtgggcaaatagtgggtgatttgataaatttggagaaatgggttctttttggcatcatgtcgtg-gtctattatatgttaatgattgat-gatgttcttagctttt--ggttgaattaattgcagCTTCCTCCTGAATGGACCGATCAGTTTGAGTCAGGCATTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttgtttgatgattgattgactcaaccaccttttgtgatgcaattaattgcagCTTCCTCCTGAATGGACAGACCAGTTTGAGTCAGGCATTCAG
aattaat putative branch site (score: 3)
aattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccagtgttgtgttttgtttttttctggtggttattatgtgtagctgttttgtttgatgattgattgactcaaccaccttttgtgatgcaattaattgcagCTTCCTCCTGAATGGACAGACCAGTTTGAGTCAGGCATTCAG
ccagtgt
- - - - -tgttttg
- - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - - - -gtagctg
- - - - - - - - - - - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgca