Sequence
atgc intronic sequence ATGC exonic sequencegtatatatctcttatgtgatttctcatactttgtgaaaaaataaaatcgtttcatgtcgtttgtactcaattgtaacactaatggactttggtttcagGATCACTTGGCATTGATGATGGAGCTTCTCGGGATGATGCCACGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G05480.1 (Glycine max), 3'ss of exon 2
gtatatatctcttatgtgatttctcatactttgtgaaaaaataaaatcgtttcatgtcgtttgtactcaattg--taacactaatggactttggtttcagGATCACTTGGCATTGATGATGGAGCTTCTCGGGATGATGCCACGAAAG
| | ||| | | || | || || | ||| | | | | | ||| | ||| | | || | |||||||| |||||||||||||||||||||| ||||||||||| || |||
ctgtgagaaatgtataaaaatgtgcaatgctgctgtgtttattaggacgtcaatttcaatctagaataaatgagttgacattttgtaatttactctacagGATCATCTGGCATTGATGATGGAGCTTCTTGGGATGATGCCTCGCAAG
upper sequence: AT5G22840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G30440.1 (Glycine max), 3'ss of exon 2
gtatatatctcttatgtgatt-tctcatact-ttgtgaaaaaataaaatc--gtttcatgtcgtttgtactcaattgtaacactaatggactttggtttcagGATCACTTGGCATTGATGATGGAGCTTCTCGGGATGATGCCACGAAAG
| | | ||| | | | || || |||| | | | | ||||| | || ||| | | ||| | | || | |||||||| |||||||||||||||||||||| ||||||||||| || |||
-tgtgcgaattgtataaaaatgtgcaatgctgctgtggttatttggacttcaatttcaatctatgaataaacaagt-tgacattttgtaatttactctacagGATCATCTGGCATTGATGATGGAGCTTCTTGGGATGATGCCTCGCAAG
upper sequence: AT5G22840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G08900.1 (Glycine max), 3'ss of exon 2
-gtatatatctcttatgtgatttctcatactttgtgaaaaaataaaatcgtttcatgtcgtttgtactcaattg-taacactaatggactttggtttcagGATCACTTGGCATTGATGATGGAGCTTCTCGGGATGATGCCACGAAAG
| | | | | ||| |||| | || | |||| | | || | | ||| | || | | || || |||||||| |||||||||||||||||||||| |||| |||||| | |||
tggaaacaaatgttacaaaatttgaaaataaaactgtctacctaaatttgaacttcaatcaatggattgttttgatgacctttaaatgtttgttttacagGATCATCTGGCATTGATGATGGAGCTTCTTGGGAAGATGCCTCCCAAG
upper sequence: AT5G22840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0061g01050.t01 (Vitis vinifera), 3'ss of exon 2
gtatatatctcttatgtgatttctcatactt---tgtgaaaaaataaaatcgtttcatgtcgtttgtactcaattgtaacactaatggactttggtttcagGATCACTTGGCATTGATGATGGAGCTTCTCGGGATGATGCCACGAAAG
| ||| | | ||| | || | | | | | || | ||| | || | || ||| | | | || | | | | ||||||||||||| |||||||||||||||| || |||||||| || |||
atttatttattttaatcaagttgataccagtagatatcagaattttgaattgatttttacttcgtg-acttagtatttcttttacttttccctatctatagGATCACTTGGCGCTGATGATGGAGCTTCTTGGAATGATGCCGCGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcgtttcatgtcgtttgtactcaattgtaacactaatggactttggtttcagGATCACTTGGCATTGATGATGGAGCTTCTCGGGATGATGCCACGAAAG
cactaat putative branch site (score: 2)
aattgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatctcttatgtgatttctcatactttgtgaaaaaataaaatcgtttcatgtcgtttgtactcaattgtaacactaatggactttggtttcagGATCACTTGGCATTGATGATGGAGCTTCTCGGGATGATGCCACGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT