Sequence
atgc intronic sequence ATGC exonic sequence...ctagttgtattcactttgctgtgcagctagctagtttgtgtaattgtgtctagtgaaaattgatgcaactgtttaattattattgatggtgattttgcagGCGCTGACGAACGGCCGGTACAAGAGCTGCCTGCACCGGGCGGTGGTGCACCGGGAGCAGGAGCGGCGGTCGCTGGCCTTCTTCCTCTGCCCGCGCGAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g34854.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g34854.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G25420.1 (Arabidopsis thaliana), 3'ss of exon 2
ctagttgtattcactttgctgtgcagct---agctagtttgtgtaattgtgtctagtga--aaattgatgcaactgtttaattattattgatggtgattttgcagGCGCTGACGAACGGCCGGTACAAGAGCTGCCTGCACCGGGCGGTGGTGCACCGGGAGCAGGAGCGGCGGTCGCTGGCCTTCTTCCTCTGCCCGCGCGAGG
|| ||| | || | | || | || | || || | | || | | | || | | || | || || || ||||| |||| || |||||| | |||||||||||| ||||||||||||||||| || | ||| ||| || || || || |||||| | || ||| | |
gtaacc-catttagatttttaaaaacctcacatcttggttagatatatacagcctttggctaggtacctccatatactaaactgggcttaatattg-ttttgtagGCTCTATCGAACGATAGATACAAGAGCTGCTTGCACCGGGCGGTGGTGAACAGCGAGAGCGAGAGGAAATCACTTGCATTCTTCTTGTGTCCGAAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtctagtgaaaattgatgcaactgtttaattattattgatggtgattttgcagGCGCTGACGAACGGCCGGTACAAGAGCTGCCTGCACCGGGCGGTGGTGCACCGGGAGCAGGAGCGGCGGTCGCTGGCCTTCTTCCTCTGCCCGCGCGAGG
tattgat putative branch site (score: 3)
aactgtttaattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagttgtattcactttgctgtgcagctagctagtttgtgtaattgtgtctagtgaaaattgatgcaactgtttaattattattgatggtgattttgcagGCGCTGACGAACGGCCGGTACAAGAGCTGCCTGCACCGGGCGGTGGTGCACCGGGAGCAGGAGCGGCGGTCGCTGGCCTTCTTCCTCTGCCCGCGCGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - -ttgctgt
- - - - - - - - - - - gcagcta
- - - - - - - - - - - - - - - - - - - - - - - - - -agtgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgg