Sequence
atgc intronic sequence ATGC exonic sequencegttcttataactccgatttaattgattaataccctattgaattagttcatgattgttaattttcgggtgtgtagacagTTGATAGATTGATTGAAACTGGAGACAGTGAGCAAATTTTCCAGAAAGCAATCAGGGAGCAAGGACGAGGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03800.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G27050.1 (Glycine max), 3'ss of exon 9
---------gttcttataactccgat---ttaattgattaataccctattgaattagttcatgattgttaattttcgggt-----------gtgtagacagTTGATAGATTGATTGAAACTGGAGACAGTGAGCAAATTTTCCAGAAAGCAATCAGGGAGCAAGGACGAGGACAG
|| | ||||| || ||| |||| | | | || ||| | | | ||| | ||| | || ||||| |||| ||||| |||||||||||||| ||||| |||||||||||||| || || ||| ||||||||||| |||
gtattctttcttttcttaactattattcattagctgatgcagagctgatggaaatgtcttttaggagtttgtcttctaatcatataactatgtacagACAATTGACAGATTAATTGAAACTGGAGATAGTGAACAAATTTTCCAGAAGGCTATTCAGGAACAAGGACGAGGCCAG
upper sequence: AT3G03800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0032g00440.t01 (Vitis vinifera), 3'ss of exon 9
------gttcttataactccgatttaattgattaataccctattgaattagttcatgattgttaattttcgggtgtgt---agacagTTGATAGATTGATTGAAACTGGAGACAGTGAGCAAATTTTCCAGAAAGCAATCAGGGAGCAAGGACGAGGACAG
|| || | || || | ||||| || | |||||||| ||||| | | | | ||||| |||| ||||| ||||| |||||||||||||| |||||||||||||||||||| ||| ||||||||||| |||
gtgaaaattattgcacctttgacatgtgaaattaacttttacatgtgatttttcatgatc--taattcttcaatattttacagACAATTGACAGATTAATTGAGACTGGAGACAGTGAACAAATTTTCCAGAAAGCAATTCAGGAACAAGGACGAGGCCAG
upper sequence: AT3G03800.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S496_4V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------------------------gttcttataact-ccgatttaattg--attaatac-cctattgaattagttcatgattgttaattttcggg-----tgtgtagacagTTGATAGATTGATTGAAACTGGAGACAGTGAGCAAATTTTCCAGAAAGCAATCAGGGAGCAAGGACGAGGACAG
| || | |||| | || || | || | || | || | | | | |||| ||| || |||| | ||||||||||| |||||||||||||||||||| || | || ||| |||||| || |||| |||
gtaagcttgtcgacccttcttctaatgcaactttcagttctatttgttagttttgaaagagaacaattgtgtacttatcttccgattgatatccatgtccatcgatcacactgtcatagttgtgcccgtcgagatctttagttaccttacaacttcgttatttttgtacagGTCATTGAACGCTTGATTGAAACAGGAGACAGTGAGCAAATTTTTCAAAGGGCTATCCAGGAGCAGGGGAGAGGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattaataccctattgaattagttcatgattgttaattttcgggtgtgtagacagTTGATAGATTGATTGAAACTGGAGACAGTGAGCAAATTTTCCAGAAAGCAATCAGGGAGCAAGGACGAGGACAG
tgttaat putative branch site (score: 3)
atgattgttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttataactccgatttaattgattaataccctattgaattagttcatgattgttaattttcgggtgtgtagacagTTGATAGATTGATTGAAACTGGAGACAGTGAGCAAATTTTCCAGAAAGCAATCAGGGAGCAAGGACGAGGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG