Sequence
atgc intronic sequence ATGC exonic sequence...tgtagccctgcacgtgtcggcctctccgttgatgaatgatgatgtatgtatgtatttttttttgtctgaaggaatttgtggggaattgttgtgtgtgcagGCGCTGTCGAACGGGAGGTATAAGAGCTGCCTGCACAGGGCGGTGGTGAACCAGCGGCGGGAGCGGCGGTCGCTGGCGTTCTTCCTGTGCCCGCGGGAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g66100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g66100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G049418_T01 (Zea mays), 3'ss of exon 2
---------tgtagccctgcacgt-gtcggcctctccgttgatgaatgatgatgtatgtatgtatttttttttgtctgaaggaatttgtggggaattgttgtgtgtgcagGCGCTGTCGAACGGGAGGTATAAGAGCTGCCTGCACAGGGCGGTGGTGAACCAGCGGCGGGAGCGGCGGTCGCTGGCGTTCTTCCTGTGCCCGCGGGAGG
| ||| || || | ||| | | ||| || |||| | | | || | || | |||| | | ||||||||||||||||||||||||| ||||||||||||||| | |||||||||||||||||||||| ||||||||||||||| ||||||||||||||||| ||||
tccggttgtcgcggcctggcccgccgccgggcgcaccgc-----aacaatgagacagcccgacacgatgattcttgtgca-----ctgtgctaacccgcatgccatgcagGCGCTGTCGAACGGGAGGTACAAGAGCTGCCTGCACCGCGCGGTGGTGAACCAGCGGCGGGCGCGGCGGTCGCTGGCCTTCTTCCTGTGCCCGCGCGAGG
upper sequence: LOC_Os01g66100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G368411_T01 (Zea mays), 3'ss of exon 2
---tgtagccctgc-acgtgtcggcctctccgttgatgaatgatgatgta-tgtatgtatttttttttgtctgaaggaatttgtggggaattgttgtgtgtgcagGCGCTGTCGAACGGGAGGTATAAGAGCTGCCTGCACAGGGCGGTGGTGAACCAGCGGCGGGAGCGGCGGTCGCTGGCGTTCTTCCTGTGCCCGCGGGAGG
|||||| | | | | ||| || | | |||| |||| || | | | ||| | || | ||||||||||||| |||||| |||| ||||||||||||||| | ||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||| ||||
cgcgacagccctaccgtccgacacgatgattcttg-tgcactgtactgtactgtac-taactccccccaccccctccggtatgtaacgcatg---ccatatgcagGCGCTGTCCAACGGGCGGTACAAGAGCTGCCTGCACCGCGCGGTGGTGAACCGGCGGCAGGAGCGGCAATCGCTGGCCTTCTTCCTGTGCCCGCGCGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtatgtatttttttttgtctgaaggaatttgtggggaattgttgtgtgtgcagGCGCTGTCGAACGGGAGGTATAAGAGCTGCCTGCACAGGGCGGTGGTGAACCAGCGGCGGGAGCGGCGGTCGCTGGCGTTCTTCCTGTGCCCGCGGGAGG
tgtatttttttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtagccctgcacgtgtcggcctctccgttgatgaatgatgatgtatgtatgtatttttttttgtctgaaggaatttgtggggaattgttgtgtgtgcagGCGCTGTCGAACGGGAGGTATAAGAGCTGCCTGCACAGGGCGGTGGTGAACCAGCGGCGGGAGCGGCGGTCGCTGGCGTTCTTCCTGTGCCCGCGGGAGG
- - -ccctgca
- - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - -atgatga
- - - - - - - - - - - - - - - - - - - - -atgtatg