Sequence
atgc intronic sequence ATGC exonic sequenceGCAGCTTTAGTGGTGGATCCAGTTATGGTGTCCACAAGTGGAGATACTCTTTCAGAATCATCTACTCTCTCTGTATATAGgtacaggattcatatttggtttgttttatttgtatttataacatccggttggaatgcttcataaaatttagtgtaatagtgcaacatttgttttgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g09000.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g09000.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G401934_T04 (Zea mays), 5'ss of exon 4
GCAGCTTTAGTGGTGGATCCAGTTATGGTGTCCACAAGTGGAGATACTCTTTCAGAATCATCTACTCTCTCTGTATATAGgtacaggattcatatttggtttgttttatttgtattta---taacatccggttggaatgct---------------tcataaaatttagtgtaatagtgcaacatttgttttgtgcag
|| ||||||||||||| || ||||||||||| || || ||||||||||||| | ||||||||||| || ||||||||||| ||| || |||| |||||| | || |||| | | | ||| | |||| || | ||| | || | || ||||| || ||||
----CTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAGgtacaagatcaatgtttgttttgttccgtatgcatttgagttcttgttggattgtattgctgtttcattgtcaatactgtagtacttatggacatgatcttgcaattgttatgagcag
upper sequence: LOC_Os12g09000.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G401934_T02 (Zea mays), 5'ss of exon 4
GCAGCTTTAGTGGTGGATCCAGTTATGGTGTCCACAAGTGGAGATACTCTTTCAGAATCATCTACTCTCTCTGTATATAGgtacaggattcatatttggtttgttttatttgtattta---taacatccggttggaatgct---------------tcataaaatttagtgtaatagtgcaacatttgttttgtgcag
|||||| ||||||||||||| || ||||||||||| || || ||||||||||||| | ||||||||||| || ||||||||||| ||| || |||| |||||| | || |||| | | | ||| | |||| || | ||| | || | || ||||| || ||||
GCAGCTCTAGTGGTGGATCCGGTCATGGTGTCCACCAGCGGTGATACTCTTTCAGGACCATCTACTCTCGCTACATATAGgtacaagatcaatgtttgttttgttccgtatgcatttgagttcttgttggattgtattgctgtttcattgtcaatactgtagtacttatggacatgatcttgcaattgttatgagcag
upper sequence: LOC_Os12g09000.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv12s0035g00320.t01 (Vitis vinifera), 5'ss of exon 4
GCAGCTTTAGTGGTGGATCCAGTTATGGTGTCCACAAGTGGAGATACTCTTTCAGAATCATCTACTCTCTCTGTATATAGgtacaggattcatatttggtttgttttatttgtatttataacatccggttggaatg-cttcataaaatttagtgtaatagtgcaacatttgttttgtgcag---
|||||||||| ||||| || |||||||| |||||||||||| || | | | || | ||| ||| || | |||| | | ||| || ||| | | || || | || | | | | | || | |||||| | | | |||| |
----CTTTAGTGGTCGATCCCGTCATGGTGTCTACAAGTGGAGATGTACTGGCTGGTCCTTCCATTCTTGCTGCATTTCGgtatgtcagttctatgtg-cacatttaagtaataatttgatgatttgagtcctttaaccttctagtgtcccatgtaattatattttaatggtttctgactacagMapped 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|58672196|gb|CK060882.1|CK060882EST: TCCACAAGTGGAGATACTCTTTCAGAATCATCTACTCTCTCTGTATATAG GGATGAATTATTTGCTATGGCTGAT
genomic: TCCACAAGTGGAGATACTCTTTCAGAATCATCTACTCTCTCTGTATATAGgtacaggatt ... ttttgtgcagGGATGAATTATTTGCTATGGCTGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCAGCTTTAGTGGTGGATCCAGTTATGGTGTCCACAAGTGGAGATACTCTTTCAGAATCATCTACTCTCTCTGTATATAGgtacaggattcatatttggtttgttttatttgtatttataacatccggttggaatgcttcataaaatttagtgtaatagtgcaacatttgttttgtgcag
- - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - GGAGAT