Sequence
atgc intronic sequence ATGC exonic sequencegtaagactaatctgatgatttttctatggttctggattattgtcttagactttatgtggttattgatttttatttacttatggaaatccagGGAACACAGATTCAGGCAACAATGTTTAACGCAGCTGCAAGGAAGTTTTATGACAGATTCGAGATGGGAAAGGTGTACTATATATCCAGGGGATCACTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08020.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 4
gtaagactaatctgatgatttttctatggttctggattattgtcttagacttta--tgtggttattgatttttatttacttatggaaa--tccagGGAACACAGATTCAGGCAACAATGTTTAACGCAGCTGCAAGGAAGTTTTATGACAGATTCGAGATGGGAAAGGTGTACTATATATCCAGGGGATCACTTA
|||||| | || | || || | || || | ||||||| | ||| | ||| |||| | ||| || || || ||||||| || |||||||||||||| |||||||| ||||||||||| |||| ||||| ||| | |||||||||| ||||| || || |||||| | | |
gtaagaattattgtgtatttattttggaattt--gaatgttgtcttgcatgttaaatctggagggtgatgtcgttttgttt-tgaaattttccagGGTACTCAGATTCAGGCAACTATGTTTAATAATGCTGCAAGGAAATTTTTTGACAAATTTGTTCTGGGAAAGGTTTACTACATTTCAAGGGGAACTTTGA
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g07440.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------gtaa-gactaatctgatgatttttctatggttctggattattgtcttagactttatgtggttattgattttt---atttacttatggaaatccagGGAACACAGATTCAGGCAACAATGTTTAACGCAGCTGCAAGGAAGTTTTATGACAGATTCGAGATGGGAAAGGTGTACTATATATCCAGGGGATCACTTA
|| |||||| | || ||| | || | ||| | || || | || | | | |||| || ||| || | | ||||| ||||| || || |||||||||||||||| ||||||||||||||| ||||| | ||| | |||| ||||| || || ||||| | ||| | || |
gtaagcagaaaaagaatccattttctgagaatgctagatactttgtgctgactaaatttgcaatattt-tgtgtgtttgggtcatatctctacaattaacatcataattgtttcagcaaattggtttctcttggtgcagGGTACACAAATCCAAGCAACAATGTTTAACGAAGCTGCAAGGAAGTTCTATGAAAAGTTCCAACTGGGGAAGGTCTATTACATATCAAAAGGAGCTCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattgtcttagactttatgtggttattgatttttatttacttatggaaatccagGGAACACAGATTCAGGCAACAATGTTTAACGCAGCTGCAAGGAAGTTTTATGACAGATTCGAGATGGGAAAGGTGTACTATATATCCAGGGGATCACTTA
tattgat putative branch site (score: 3)
ttattgatttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagactaatctgatgatttttctatggttctggattattgtcttagactttatgtggttattgatttttatttacttatggaaatccagGGAACACAGATTCAGGCAACAATGTTTAACGCAGCTGCAAGGAAGTTTTATGACAGATTCGAGATGGGAAAGGTGTACTATATATCCAGGGGATCACTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG