Sequence
atgc intronic sequence ATGC exonic sequencegtattattttgtattttgtatcagttaaattcgttcatttaccaatatggatcgacgtgtcatcttcttttgctgcaatttacctaattgtctactgctttcagCTGGCTAATACAGAGGAGTATATTGATGGGCAATTCTCTGGAAACTTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g08090.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g08090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 3
gtattattttgt--attttgtatcagttaaattcgttcatttaccaatatggatcgacgtgtcat-cttcttttgctgcaatttacctaattgtctactgctttcagCTGGCTAATACAGAGGAGTATATTGATGGGCAATTCTCTGGAAACTTGG----------------
||| || |||| ||| | || || | | | || || || | | || ||| | || ||| | | || || | ||||| | ||||| || ||||| |||||||| |||||||||||||||||||||||| |||
gtactaatttgacagtttagctgttgtactgttagagtgatcatcactagggtactaaatgacatacaaaattcattgc---tgccttatttttgtactg--tgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG
upper sequence: LOC_Os02g08090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G058252_T01 (Zea mays), 3'ss of exon 3
----------------------------------gtattattttgtattt--tgtatcagttaaat--tcgttcatttaccaa-tatggatcgacgtgtcatcttcttttgctgcaatttacctaattgtctactgctttcagCTGGCTAATACAGAGGAGTATATTGATGGGCAATTCTCTGGAAACTTGG----------------
| | | |||||| || | || | ||| |||| || || || ||| | | ||| || ||||| | | || |||||||| | ||||| || || || |||||||| |||||||| ||||||||||||||| |||
gtactaatttggcagtttggctgtcatactataagggtggtggtgtattgaatgcgtgagatgaatagctaatcatctattgggtactgaatgacatacaaaattcatt-gctgc----ctcttttttttctactgcgtgcagCTTGCCAACACTGAGGAGTACATTGATGGTCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|88338829|gb|CI677236.1|CI677236EST: GATATCTTGTTTCTGTCGACTCTTATATGAATCTGCAG CTGGCTAATACACAGGAGTATATTGATGGGCCATCCTCTGGAAACTCGGGT
genomic: GATATCTTGTTTCTGTCGACTCTTATATGAATCTGCAGgtattatttt ... ctgctttcagCTGGCTAATACAGAGGAGTATATTGATGGGCAATTCTCTGGAAACTTGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcgacgtgtcatcttcttttgctgcaatttacctaattgtctactgctttcagCTGGCTAATACAGAGGAGTATATTGATGGGCAATTCTCTGGAAACTTGG
acctaat putative branch site (score: 3)
ctgctttc putative PPT
aattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattattttgtattttgtatcagttaaattcgttcatttaccaatatggatcgacgtgtcatcttcttttgctgcaatttacctaattgtctactgctttcagCTGGCTAATACAGAGGAGTATATTGATGGGCAATTCTCTGGAAACTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG