Sequence
atgc intronic sequence ATGC exonic sequencegtatgctattaggatttttcgctatatacgtattcagttttgcgacgtcttcatggtctctgatcgattttattggattcagGTGAATGCAAGTGGCCAATTCTGCGGTGTAGCTGAGATGATTGGACGAGTTGATTATGAGAAAAGCATGGAGTTCTGGCAACAAGATAAGTGGACTGGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79270.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g48790.3 (Oryza sativa), 3'ss of exon 3
------------gtatgctattaggatttttcgctatatacgtattc--agttttgcgacgtcttcatg--gtctctgatcg--attttattggattcagGTGAATGCAAGTGGCCAATTCTGCGGTGTAGCTGAGATGATTGGACGAGTTGATTATGAGAAAAGCATGGAGTTCTGGCAACAAGATAAGTGGACTGGCT
| || || | | |||||| | | | | | ||| || | | | ||| || | ||| |||||||| ||||||||||| |||||||| || ||||||||| | || | || |||| | | | ||| | |||||||| || || ||||||| ||| |
tgagttcatggttcaccctttttttgtggggggaaatatacttttgccaattcttgtaactttgttgtaaaacttctaattattacactatgatgaccagGTGAACGCAAGTGGCCAGTTCTGCGGCGTGGCTGAGATGGTCGGTCCGGTAGATTTCAACAGGAATATGAACTTCTGGCAGCAGGACAAGTGGAATGGAT
upper sequence: AT1G79270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G17240.1 (Glycine max), 3'ss of exon 6
------------------------------------gtatgctattaggatttttcgctatatacgtattcagttttgcga----------cgtcttcatggtctctgatcgat--tttattggattcagGTGAATGCAAGTGGCCAATTCTGCGGTGTAGCTGAGATGATTGGACGAGTTGATTATGAGAAAAGCATGGAGTTCTGGCAACAAGATAAGTGGACTGGCT
||| | | ||| || ||| | ||||| || | | || | | || | | || ||| ||||||| ||||| ||||| ||||| ||||| ||||||||||||| |||||||||||||| | ||||| ||||| ||||||||||| |||||||||| ||| |
gtatgcaatttgggtccatcgcaaaaacttcagatcccctgcacccatgttttctctgcttatgtattttcagattgacaagtgataactgtgtttcttaacttcctttctggtaattgcttgtgttcagGTCAATGCTAGTGGTCAATTTTGCGGAGTAGCTGAGATGACTGGACGAGTTGATTTCAACAAAAGTATGGATTTCTGGCAACAGGATAAGTGGAATGGAT
upper sequence: AT1G79270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv19s0085g01100.t01 (Vitis vinifera), 3'ss of exon 6
----gtatgctattagg-atttttcgctatatacgtattcagttttgcgac-----gtcttcatggtctctgatcg-attttattggattcagGTGAATGCAAGTGGCCAATTCTGCGGTGTAGCTGAGATGATTGGACGAGTTGATTATGAGAAAAGCATGGAGTTCTGGCAACAAGATAAGTGGACTGGCT
|| | ||| | ||| | ||| | | |||| || | | || | | || | | || || |||| ||||||||||| || ||||| || ||||||||||||||||| |||||||||| | | || | |||||| ||||||||||| |||||||||| ||| |
gtaagtttagaatttgatgtttctggctggaaaattattttccctttcatccaataaattttaattcatttgtccatgtattgccatgtttagGTTAATGCAAGTGGGCAGTTCTGTGGAGTAGCTGAGATGATTGGCCGAGTTGATTTTAATAAGAACATGGACTTCTGGCAACAGGATAAGTGGAATGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgtattcagttttgcgacgtcttcatggtctctgatcgattttattggattcagGTGAATGCAAGTGGCCAATTCTGCGGTGTAGCTGAGATGATTGGACGAGTTGATTATGAGAAAAGCATGGAGTTCTGGCAACAAGATAAGTGGACTGGCT
ctctgat putative branch site (score: 4)
ttttatt putative PPT
attttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctattaggatttttcgctatatacgtattcagttttgcgacgtcttcatggtctctgatcgattttattggattcagGTGAATGCAAGTGGCCAATTCTGCGGTGTAGCTGAGATGATTGGACGAGTTGATTATGAGAAAAGCATGGAGTTCTGGCAACAAGATAAGTGGACTGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA