Sequence
atgc intronic sequence ATGC exonic sequence...tatggtgattgtaaaggttgaaatttaaaattctgaaggtttcattttgatgattcaaaattatgccacaactactgatgttcaaatattattttcccagGTTTCAGATACAGATCATATTGACAGGTTTATATCATGCCTGCAAACGGCCCTTCCATTCTTTGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G29030.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G29030.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G24090.2 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------------------------tatggtgattgtaaaggttgaaatt---taaaattctgaaggtttcattttgat---gattcaaaattatg-ccacaactactgatgttcaaatattattttcccagGTTTCAGATACAGATCATATTGACAGGTTTATATCATGCCTGCAAACGGCCCTTCCATTCTTTGCA
| | | ||| || | ||| | || || | ||| | | | |||| || | | || || || | || |||| | ||| |||| |||||| ||||||||||||||||||| ||||||||||| || | ||| |||||||| | |
gtgattattatttttttttcttttcttattcaacacacaaatacagtcattttatatgtaaaaagaatctgttttgaattagtaaaatggtctcttaattttagactttgctgctggcagaagttattaagtaatggaagtagtatagattttgttttggggtctcatgtaatggtttttaaatggaaatttgt-agGTATCAGATGCAGATCATATTGACAGGTTGATATCATGCCTTCATATGGCACTTCCATTTGTAGTG
upper sequence: AT1G29030.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G32480.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------------------------tatggtgattgtaaa-----ggttgaaatt-taaaattctgaaggtttcattttgatgattcaaaattatgccacaactactgatgttcaaatattattttcccagGTTTCAGATACAGATCATATTGACAGGTTTATATCATGCCTGCAAACGGCCCTTCCATTCTTTGCA
| | ||||| | | || |||| || | || | || | || || | ||| | | | || || || | || |||| | ||| |||| |||||| |||||||||||||| |||| ||||| ||||| || | ||| |||||||| |||
gtaattattattctttttttcttttctttcatccagttgagcacgcaaatacaatcattttatatgtaagagaaatctgttttgtattagtaaaatggtctcttgattttttactgctggctgaagttattaagtagtgtaagtagtat----agatttcgttttggggtctcatgtaatggtttttaaatggcaattttt-agGTATCAGATGCAGATCATATTGACCGGTTGATATCTTGCCTTCACATGGCACTTCCATTTGTTGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatgattcaaaattatgccacaactactgatgttcaaatattattttcccagGTTTCAGATACAGATCATATTGACAGGTTTATATCATGCCTGCAAACGGCCCTTCCATTCTTTGCA
tactgat putative branch site (score: 2)
ttattttccc putative PPT
atgttcaaatattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatggtgattgtaaaggttgaaatttaaaattctgaaggtttcattttgatgattcaaaattatgccacaactactgatgttcaaatattattttcccagGTTTCAGATACAGATCATATTGACAGGTTTATATCATGCCTGCAAACGGCCCTTCCATTCTTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaacta