Sequence
atgc intronic sequence ATGC exonic sequencegtaagattttaatgaagcttacagtacctaagattttaagaagaaatgcatgcatctggtgtaagagactttgtaattgtaattgattgtgtaattgtaaaatactgttcaatattttctatgtatcctctacttttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G47550.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
gtaagattttaatgaagcttacagtacctaagattttaagaagaaatgcatgcatctggtgtaagagactttgtaattgtaat-tgattgtgtaattgtaaaatactgttcaatattttctatgtatcctctacttttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG
| | | | | || | ||| | | | || |||||| || || | | | ||| || || |||| | | ||| | || ||||||||||||| || || ||||| |||||||| |||||||| ||||| |||||||||| |||||||||
---------------------------------------------------gtacttacttt----gatccctcatttgcattgtctttctgtaatagttaataaaagct-aatggctt--atcctcttctaacttgttgttatgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 3
gtaagattttaatgaagcttacagtacctaagattttaagaagaaatgcatgcatctggtgtaagagactttgtaattgtaattgattgtgtaattgtaaaatactgttcaatattttctatgtatcctctacttttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG
|| | || || | | || | | | ||| | || || | | ||| | || || ||| | |||| |||||||||||||| || || || || ||||| ||||||||||||||||| |||||||| ||||||||
--------------------------------------------------------------gtaagtttctggaacagaagcaaatcaggattcaaccatttcctgctatgtagcttgtttctatt---tgctgatgaatatgta---tcttatagGGGTTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCACAGTGGACAATGCGCAATGTCGATGACAG
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattttaatgaagcttacagtacctaagattttaagaagaaatgcatgcatctggtgtaagagactttgtaattgtaattgattgtgtaattgtaaaatactgttcaatattttctatgtatcctctactt-ttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG
| || | | | || |||| | ||| || | | || | | | ||| | | || || |||| || ||| | ||||| |||||||||||||| || || ||||| ||||| || |||||||| |||||||| | |||||||||
----------------------------------------------------------gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttgtggtttctccatcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactgttcaatattttctatgtatcctctacttttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG
tgctgat putative branch site (score: 3)
tctttt putative PPT
aatattttctatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattttaatgaagcttacagtacctaagattttaagaagaaatgcatgcatctggtgtaagagactttgtaattgtaattgattgtgtaattgtaaaatactgttcaatattttctatgtatcctctacttttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA