Sequence
atgc intronic sequence ATGC exonic sequencegtaggtgctgttctggagatgtatttctcataagtcgttgagtttgtatctaaatggctttttgttttctgtctcacagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65410.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G889923_T02 (Zea mays), 3'ss of exon 2
--------------------gtaggtgctgttctg-gagatg-tatttctcataagtcgttgagtttgtatctaaatggctttttgtttt-ctgtctcacagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT
|| | |||| || || ||| || | || | | |||| || || | ||| | ||| |||||| ||||| ||||| || || |||||||| || ||||||||||||||||||| || || |
gtacatattccttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagctt--cttgtgcctgaacattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G868168_T04 (Zea mays), 3'ss of exon 5
---------gtaggtgctgttctggagatgtatt------tctcataagt-cgttgag----tttgtatctaaatggctttttgtttt-ctgtctcacagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT
| ||||| | || | |||| | | ||| | | | ||| |||| || | | ||| | ||| |||||| ||||| ||||| || || |||||||| || ||||||||||||||||||| || || |
gtacatattctttgtgctttgttgcatctgtactaagaaatggcatgatttccttgtagcttcttgtgcctgagcattctgatgtggtgttgtgatacagGTCTTTCAAAGTGCTGCACTTTTTGATTCTCTCACAGTTCGTGAAAATGTTGGATTCCTTTT
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 4
gtaggtgctgttctggagatgtatttctcata--agtcgttgagtttgtatctaaatggctttttgttttctgtct---cacagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT
|| ||| ||| ||| ||| | | || || | || | | ||| || |||| ||| | |||| || || |||||||| ||||||||||| | | ||||||||||||||||||||||| |
----gtaa-gtttcagagtattatgcaatatactaattcttattttgttttcaacgtaacttattttttttaatctgtaaatagGTTTTCCAAAGTGCAGCACTCTTTGATTCTTTGACTGTTCGTGAAAATGTTGGTTTTCTCTT
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 4
gtagg-tgctgtt---ctggagatgtatttc----tcataagtcgttgagtttgtatctaaatggctttttgttttctgtctc----acagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT
||| | || || || || | | || || ||||| | ||| || | | | | | || | || |||||| ||||||||||| || || |||||||| || | |||||||||||||||||||| || |
gtaaaatacttttaaactttaggtattctttcctgtcctaagttatcatatttctaatcatgtaattctgttttcttctcttctgaaacagGTCTTTCAGAGTGCTGCACTTTTTGATTCTTTAACTGTTCGTGAAAATGTTGGTTTCCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcataagtcgttgagtttgtatctaaatggctttttgttttctgtctcacagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT
atctaaa putative branch site (score: 3)
ctttttgttttctgtc putative PPT
tttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtgctgttctggagatgtatttctcataagtcgttgagtttgtatctaaatggctttttgttttctgtctcacagGTATTTCAGAGTGCAGCTCTCTTTGATTCACTATCAGTTCGTGAAAATGTTGGTTTTCTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC