Sequence
atgc intronic sequence ATGC exonic sequencegtacgcgtgctccgcgcgtcgcgtctcattcacagtcatgctgtcctttctacactcgcacgcttgacacaaccaaggtgttcccttccccgtgacgcgcgtgcagGGCTGCGACGCCTCGGTGCTCCTGGACCGCATCAACGGCGACAAGTCGGAGAGGGAAGCGGCCCCGAACCAGTCGCTGAGAGGCTTCGGCGCCGTCGACA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g51550.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g51550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G067096_T05 (Zea mays), 3'ss of exon 1
gtacgcgtgctccgcgcgtcgcgtctcattcacagtcatgctgtcctttctacactcgcacgcttgacacaaccaaggtgttcccttccccgtgacgcgcgtgcagGGCTGCGACGCCTCGGTGCTCCTGGACCGCATCAACGGCGACAAGTCGGAGAGGGAAGCGGCCCCGAACCAGTCGCTGAGAGGCTTCGGCGCCGTCGACA
| | | || | | ||| | | | | ||| | | || |||||||||||||||||||||||||||| ||||||||| || |||| | | |||||| | || || | ||||||||||||||| | ||| | |||||||||||
---------------------------------gtacgtacgtcggttcttgctgctgcatgtcttgtgt---ctgtgaactccatgtcgacgatcgagcgtgcagGGCTGCGACGCCTCGGTGCTGCTGGACCGCGTCGGCGGCCAGAGATCGGAGCGCGACGCCGGCCCGAACCAGTCGCTTCGCGGCCTGGGCGCCGTCGAGG
upper sequence: LOC_Os01g51550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G067096_T09 (Zea mays), 3'ss of exon 1
gtacgcgtgctccgcgcgtcgcgtctcattcacagtcatgctgtcctttctacactcgcacgcttgacacaaccaaggtgttcccttccccgtgacgcgcgtgcagGGCTGCGACGCCTCGGTGCTCCTGGACCGCATCAACGGCGACAAGTCGGAGAGGGAAGCGGCCCCGAACCAGTCGCTGAGAGGCTTCGGCGCCGTCGACA
| | || | | ||| | | | | ||| | | || |||||||||||||||||||||||||||| ||||||||| || |||| | | |||||| | || || | ||||||||||||||| | ||| | |||||||||||
-------------------------------------gtacgtcggttcttgctgctgcatgtcttgtgt---ctgtgaactccatgtcgacgatcgagcgtgcagGGCTGCGACGCCTCGGTGCTGCTGGACCGCGTCGGCGGCCAGAGATCGGAGCGCGACGCCGGCCCGAACCAGTCGCTTCGCGGCCTGGGCGCCGTCGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acactcgcacgcttgacacaaccaaggtgttcccttccccgtgacgcgcgtgcagGGCTGCGACGCCTCGGTGCTCCTGGACCGCATCAACGGCGACAAGTCGGAGAGGGAAGCGGCCCCGAACCAGTCGCTGAGAGGCTTCGGCGCCGTCGACA
gcttgac putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcgtgctccgcgcgtcgcgtctcattcacagtcatgctgtcctttctacactcgcacgcttgacacaaccaaggtgttcccttccccgtgacgcgcgtgcagGGCTGCGACGCCTCGGTGCTCCTGGACCGCATCAACGGCGACAAGTCGGAGAGGGAAGCGGCCCCGAACCAGTCGCTGAGAGGCTTCGGCGCCGTCGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG