Sequence
atgc intronic sequence ATGC exonic sequence...acttttttttttaaaaaaaaacaattctatggtgttatttagtatacaacattgttgtccatactagcatcctaaccattgggaacaactttctttacagCGGGTCAAAAATATTTTCCACCTTTATTGGTTTCCTTAAAAGCAAAGATCCGAATGATGGAACAGAACAGGCACTGCTTAGTGAGCTGACTTCATTCGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g12630.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g12630.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G826194_T02 (Zea mays), 3'ss of exon 3
acttttttttttaaaaaaaaacaatt-ctatggtgttatttagtataca---acattgttgtccatactagcatcctaaccattgggaacaactttctttacagCGGGTCAAAAATATTTTCCACCTTTATTGGTTTCCTTAAAAGCAAAGATCCGAATGATGGAACAGAACAGGCACTGCTTAGTGAGCTGACTTCATTCGAT
| | | || | || | | | |||||| || | | ||| | | | || || || |||| |||| ||| || |||| |||||| || ||||||||||||||||| || ||||||||||| |||||||||||||| | |||||||||||| ||||||| |||| |||||| |||||||| |||
----tcatctacaacttttgcctgttattttatttttattttgttaatactcacagttctattattatgagtgtcataactattgtgaataaatttcattacagTGGATCAAAAATATTTTCCACTTTCATTGGTTTCCTCAAAAGCAAAGATCCAAGCGATGGAACAGAAGAGGCACTACTTAATGAGCTTACTTCATTTGAT
upper sequence: LOC_Os06g12630.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G04510.1 (Glycine max), 3'ss of exon 3
-----acttttt-tttttaaaaaaaaacaattctatggtgttatttagtatacaacattgttgtccatactagcatcctaaccat-tgggaacaactttctttacagCGGGTCAAAAATATTTTCCACCTTTATTGGTTTCCTTAAAAGCAAAGATCCGAATGATGGAACAGAACAGGCACTGCTTAGTGAGCTGACTTCATTCGAT
||||||| || || | ||| ||| | ||| | | ||| || ||| | | | | | | | || || ||| || |||||||| || ||||| || |||||||| || || || ||||| ||||| |||||||||||||| || ||| | || ||||| |||| || ||| |
tgtcaactttttattctttcatgtttacacaactacattaaaattaaatgtactcca--attgcctaaagtg----tatggctgtatgcatgtgttttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATCCCAATGATGGAACAGAGCAAGCATTACTAAGTGAACTGAGCTCTTTCAA-
upper sequence: LOC_Os06g12630.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G33700.2 (Glycine max), 3'ss of exon 3
acttttttttttaaaaaaaaacaattctatggtgt-tatttag-tatacaacattgttgtccatactagcatcctaaccat-tgggaacaactttctttacagCGGGTCAAAAATATTTTCCACCTTTATTGGTTTCCTTAAAAGCAAAGATCCGAATGATGGAACAGAACAGGCACTGCTTAGTGAGCTGACTTCATTCGAT
| | | | ||||| || || || | | |||| | ||| || || | | | | || ||| | | || |||||||| || ||||| || ||||||||||| || || ||||| ||||| ||||||||||||||||| ||| | |||||||| |||| || ||| |
---ctactacgtgtcagttttttattctttgatgcatacatggctatattaaatttaaacgcacacaattgcctaatgtgtatgcatgtgtttttttctttagGGGGTCAAAGATCTTTTCAACATTTATTGGTTTTCTCAAGAGCAAGGATCCCAATGATGGAACAGAACAAGCATTACTTAGTGAACTGAGCTCTTTCAGT
upper sequence: LOC_Os06g12630.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0006g00630.t01 (Vitis vinifera), 3'ss of exon 3
-acttttttttttaaaaaaaaacaattctatggtgttatttagtatacaacattgttgtccatactagcatcctaaccat-tgggaacaactttctt-tacagCGGGTCAAAAATATTTTCCACCTTTATTGGTTTCCTTAAAAGCAAAGATCCGAATGATGGAACAGAACAGGCACTGCTTAGTGAGCTGACTTCATTCGAT
| | |||| || | |||| || | | || || | | | | ||||| || | | | | | ||||||| | | || ||||| || || || | | |||||||||||||||||||||||||| || | |||||| ||||| ||| || | || | ||||| |||| || |||
catatcccattttctaattttataattaaat--tccaaatttgtg-gtagtttgagtttatgtactacaatttttatcttatatattcaactttttcctgtagTGGGTCTAAGATCTTCCCTGCATTTATTGGTTTCCTTAAAAGCAAAGACCCCAGTGATGGGACAGAGCAGACATTACTGAACGAGCTAGCTTCTTTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaacattgttgtccatactagcatcctaaccattgggaacaactttctttacagCGGGTCAAAAATATTTTCCACCTTTATTGGTTTCCTTAAAAGCAAAGATCCGAATGATGGAACAGAACAGGCACTGCTTAGTGAGCTGACTTCATTCGAT
tcctaac putative branch site (score: 1)
ctttctttac putative PPT
tttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttttttttttaaaaaaaaacaattctatggtgttatttagtatacaacattgttgtccatactagcatcctaaccattgggaacaactttctttacagCGGGTCAAAAATATTTTCCACCTTTATTGGTTTCCTTAAAAGCAAAGATCCGAATGATGGAACAGAACAGGCACTGCTTAGTGAGCTGACTTCATTCGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA