Sequence
atgc intronic sequence ATGC exonic sequencegtacttgaaacctaaaacaccaattgcaatgtattattgtattaaaataagtacaataatggttaaactattattaacaaaatgttgaaaatcgaatgtacgtagGAGCTGCAATATTTGACATGGAATATGGGAGATGGCTAGAGGATGATAACCGGCATATGTCGGAGATTCGAACCGGTCTTCAGGCTCATTTATCTGACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08320.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 9
gtacttgaaacctaaaacacca-attgcaatgtattattgtattaaaataagtacaataatggttaaactattattaacaaaatgttgaa----aatcgaatgtacgtagGAGCTGCAATATTTGACATGGAATATGGGAGATGGCTAGAGGATGATAACCGGCATATGTCGGAGATTCGAACCGGTCTTCAGGCTCATTTATCTGACAA
| ||||| | | | | | | | || | || | |||| | | | | | || | || | | ||| |||||||||||||| ||||||||||| |||| |||||| | ||||||||| | ||||| ||| |||| | || | || || |||| | | | |||
---------aaaaaaaactttatactataccaaaatgtcacatagtagcaaatgcaatgttattattatggtaactagtggagcattaatttgtggtacggtgt-tgtagGAGCTGCAATGTTTGACATGGAGTATGCAAGATGGTTGGAGGATGATCAGCGGCACATGATGGAGCTCCGTTCGGGGCTGCAGGTGCCGCTGCCGGACGG
upper sequence: AT1G08320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G19030.1 (Glycine max), 3'ss of exon 6
gtacttgaaacctaaaacacca-attgcaatgtattattgtattaaaataagtacaataatggttaaactattat--taacaaaatgttga--aaatcgaatgtacgtagGAGCTGCAATATTTGACATGGAATATGGGAGATGGCTAGAGGATGATAACCGGCATATGTCGGAGATTCGAACCGGTCTTCAGGCTCATTTATCTGACAA
||| ||||| | | || | | | | || | || | || | | ||||||||| ||||||| ||| | || | | |||||||||||||| ||||||||||| |||| | |||| |||||||||| | ||||| || |||| | || | || || ||| | | | || |||
-------aaaaacaaaactttatactgtaccaaaatgtcacat---agtagcaatgttatttttctaactattatggtaacaaagtgtgcattaatttgtggtgttgtagGAGCTGCAATGTTTGACATGGAGTATGCAAAATGGTTAGAGGATGACCAGCGGCACATAGTGGAGCTCCGGTCGGGGCTGCAGACGCCGCTGTCGGACGG
upper sequence: AT1G08320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 8
---gtacttgaaacctaaaacaccaattgcaatgtattattgtattaaaataagtacaataatggttaa-actattattaacaaaatgttgaaaatcgaatgtacgtagGAGCTGCAATATTTGACATGGAATATGGGAGATGGCTAGAGGATGATAACCGGCATATGTCGGAGATTCGAACCGGTCTTCAGGCTCATTTATCTGACAA
|| | || | || ||| | | || | | | | | || | || |||||| | || ||| | | |||||||||||| ||||| |||||||||| |||||||| ||||||||| ||||||| ||||||||| || |||| || | ||||| ||||| | ||
cacaagggtggtgtccaatgggcagcttccaacttgactcttcataagatagactcttgttatcactgttgcttttattattatgattttggtctt---------gcagGAGCTGCAATCTTTGATATGGAATATGCAAGATGGCTCGAGGATGATCACCGGCACATGTCGGAGCTTAGAACAGGCTTGCAGGCGCATTTGTTGGATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacaataatggttaaactattattaacaaaatgttgaaaatcgaatgtacgtagGAGCTGCAATATTTGACATGGAATATGGGAGATGGCTAGAGGATGATAACCGGCATATGTCGGAGATTCGAACCGGTCTTCAGGCTCATTTATCTGACAA
tattaac putative branch site (score: 1)
ttaaactattattaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgaaacctaaaacaccaattgcaatgtattattgtattaaaataagtacaataatggttaaactattattaacaaaatgttgaaaatcgaatgtacgtagGAGCTGCAATATTTGACATGGAATATGGGAGATGGCTAGAGGATGATAACCGGCATATGTCGGAGATTCGAACCGGTCTTCAGGCTCATTTATCTGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT