Sequence
atgc intronic sequence ATGC exonic sequence...agaatctaaactattttgggagagttgaaaataagatgtagtatatgtgtcactctccatgcatgtcacgtgctaatttttgtatcatgtggttacgtagGTGTCCGTCATCGCGCCCAACACGCCGGCGCTGTACGAGATGCACTTCGCCGTGCCGATGGCCGGAGCGGTGCTGAACGCCATCAACACCCGCCTCGACG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g38350.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g38350.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G05110.1 (Glycine max), 3'ss of exon 1
agaatctaaactattttgggagagttgaaaata-agatgtagtatatgtgtcactctccatgcatgtcacgtgctaatttttgtatcatgtggttacgta---gGTGTCCGTCATCGCGCCCAACACGCCGGCGCTGTACGAGATGCACTTCGCCGTGCCGATGGCCGGAGCGGTGCTGAACGCCATCAACACCCGCCTCGACG
| | | || || || | | | | ||| | || || ||||| | | | | || || | | | | | | || | ||| | | ||| || || | || || |||| || || |||| |||||||| ||||| ||||| ||||| || || ||||||||| ||||||||||||| || ||
aaaggattaattaatt-aattgtctggtatatatatatata-tatatatatatatatatatacacactaataattggtataacttttttg-gtttatgcaacaGGTATCAGTGCTGGCCCCTAACATCCCAGCAATGTATGAGATGCATTTCGCAGTGCCTATGGCAGGTGCTGTGCTGAACACCATCAACACCCGTCTTGAT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtcactctccatgcatgtcacgtgctaatttttgtatcatgtggttacgtagGTGTCCGTCATCGCGCCCAACACGCCGGCGCTGTACGAGATGCACTTCGCCGTGCCGATGGCCGGAGCGGTGCTGAACGCCATCAACACCCGCCTCGACG
tgctaat putative branch site (score: 2)
taatttttgtatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaatctaaactattttgggagagttgaaaataagatgtagtatatgtgtcactctccatgcatgtcacgtgctaatttttgtatcatgtggttacgtagGTGTCCGTCATCGCGCCCAACACGCCGGCGCTGTACGAGATGCACTTCGCCGTGCCGATGGCCGGAGCGGTGCTGAACGCCATCAACACCCGCCTCGACG
- - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcatgt