Sequence
atgc intronic sequence ATGC exonic sequencegttgacattctttcctttctatattcatttactgaagtgaactgtaatcttccttgtctaaatgcatgtcacatcttttcttaactctcagCTGAATACTTCAAGGATCGAACTGATGTCCAGTGCCTCCACAGGTGGCAAAAGGTCCTTAATCCTGAACTTGTTAAAGGGCCCTGGACGAAGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G11510.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G26240.1 (Glycine max), 3'ss of exon 4
---------gttgacattctttcctttctatattcatttactgaagtgaactgtaatcttccttgtctaaatgcatg-tcacatcttttcttaactctcagCTGAATACTTCAAGGATCGAACTGATGTCCAGTGCCTCCACAGGTGGCAAAAGGTCCTTAATCCTGAACTTGTTAAAGGGCCCTGGACGAAGGAG
|| | | | | | | | || ||| |||| |||| || |||| | || | | | | | | |||||||| ||||||||| |||||||||| || ||||| || |||||||| || || | |||||||||||||||||||| || ||| | || |||
cacctcaatgtcgcggtggtcacactgattt-ttagcttatccaagtttttcataatgttttttgtttgcctgtctaattgccaaatatacgtgtttgtagCTGAATGTTTCAAGGATAGAACTGATGTGCAATGCCTACATAGGTGGCAGAAAGTTTTAAATCCTGAACTTGTTAAAGGTCCATGGTCTAAAGAG
upper sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 3
-------------gttgacattctttcctttctatattcattt--actgaagtgaactgtaatcttccttgtctaaatgcatgtcacatcttttcttaactctcagCTGAATACTTCAAGGATCGAACTGATGTCCAGTGCCTCCACAGGTGGCAAAAGGTCCTTAATCCTGAACTTGTTAAAGGGCCCTGGACGAAGGAG
||| | | || ||| || || | | | | | || ||| | |||| ||| | ||||||||| ||||||||||| || ||||| ||||| | ||||||||||| || ||| | ||||||||||| | ||||| || ||| | || |||
caatcataatggagttaatctgtgggagaaggaatgggagttttaacagagataagttatttcacaaacttccttaatatgtaaaccatc------taatttgcagCTGAATGTTTCAAGGATCGGACCGATGTTCAGTGTTTGCACAGGTGGCAGAAAGTCTTAAATCCTGAACTCATCAAAGGTCCATGGTCTAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaactgtaatcttccttgtctaaatgcatgtcacatcttttcttaactctcagCTGAATACTTCAAGGATCGAACTGATGTCCAGTGCCTCCACAGGTGGCAAAAGGTCCTTAATCCTGAACTTGTTAAAGGGCCCTGGACGAAGGAG
tcttaac putative branch site (score: 2)
tcttttcttaactctc CT-rich tract
ttttcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgacattctttcctttctatattcatttactgaagtgaactgtaatcttccttgtctaaatgcatgtcacatcttttcttaactctcagCTGAATACTTCAAGGATCGAACTGATGTCCAGTGCCTCCACAGGTGGCAAAAGGTCCTTAATCCTGAACTTGTTAAAGGGCCCTGGACGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG