Sequence
atgc intronic sequence ATGC exonic sequenceTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttccttctattcaacaacaggggtgaatatgggggcatcctaatagttggctcactc...
Basic information
species | Oryza sativa |
transcript | LOC_Os02g36740.4 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 2
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttcct--tctattcaacaacaggggtgaatatgggggcatcctaatagttggctcactc
|| ||||| ||||||||||||||| ||||||||||||||||||| || | |||||||||||||||||| | ||||| |||| || | | | | || ||| | | || || || | || | | | || ||| | || | |
TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaattgtttccttcagctactactctaaatatatcaaaatggaaattaatgcatgcactgttttgtaatttcttgtataataagacttaaag-att-
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G118957_T04 (Zea mays), 5'ss of exon 4
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttccttctattcaacaacaggggtgaatatgggggcatcctaatagttggctcactc---
|| ||||| || |||||||||||| | |||||||||||||||||||| |||||||||||||||||||| | ||||| |||| || | | | | || | || | | || | | |||| | | | | || | | | || | |
TATGCTCACAGGGAATGTGTGCAACGTTGGTGCAATGAGAAAGGAGATATAATCTGTGAAATCTGCCATGAGgtaaccaattgtttccttcaactactactccaaacgtagcaaaatgtattgttttggcgaaagggcc---tctagcgtaatggttaaaaatgtattgttaagg
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA07G35750.2 (Glycine max), 5'ss of exon 2
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgc--tttagttccttgtggcataatttgttccttctattcaacaacaggggtgaata-tgggggcatcctaata-gttggctcactc-----------------------------------------------------------------------------------------
|| ||||||||| | || || || | |||||||||||||||||||||||||| ||||| || || || |||| | | | |||| ||| ||||| || | || || ||| | || | ||| || || | || ||| | |
TATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAGgtatggttcttatacatgtgatttttacttttgtgaaatttatggtattttaaatttgtggtgatggttagataatgctaatatggtcatgcattgttttaactagtaagctttattgaacaattattttgttcaattgtgtgtctcagtggtgtgtactaaattctttcaattttatatatgtaattctcag
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G04870.1 (Glycine max), 5'ss of exon 2
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttccttctattcaacaacaggggtgaatatgggggcatcctaatagttggctcactc-----------------------------------------------------------------------------------
|| ||||||||| | || || || | ||||||||||||||||||||||||| ||||| || || ||| |||| | | ||| ||| | | | | | | ||||| | |||| | | | | ||| | || ||| |||| || | | ||
TATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAACTTGTGAGATATGTCACAAGgtatgattcttttgtatgtgattttcgcatatagtgaaattt----ttgttatttgaaatttgtgatgatggtctggtcatggtaatgattcaattattctgtacaatggtatctctggattgaaccaaatgctctgtgtgtgtgtactgaatttctttcaattttgtatatgtaattctcag
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 3
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttccttctattcaacaacaggggtgaatatggggg---catcctaatagttggctcactc
| |||||||| ||||||| ||| |||||||||||||||||||||| ||| || || ||||| || |||| | | ||| | | || | | | | | | | | | | | || |||| | | || |||||| | ||
TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttgcttcttaattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatattaataggtaataca---
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttccttctattcaacaacaggggtgaatatgggggcatcctaatagttggctcactc--------
|| |||||||| | ||||| ||| |||||||||||||||||||||||||||| ||||| |||||||| |||| | || | | ||| |||||| || | ||| | | | || | | | || | | | | ||| || |
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgta-----tactcgt-tattttttttcctttc--cactttctgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagtMapped 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|3767112|gb|AU031222.1|AU031222EST: AAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG TCATACAAGCCTGGCTATACTGCCCCACCCCAGGTACATCATGATGAGACT
genomic: AAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaatt ... tgttgttcagTCATACAAGCCTGGCTATACTGCCCCACCCCAGGTACATCATGATGAGACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttccttctattcaacaacaggggtgaatatgggggcatcctaatagttggctcactc
- - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - AGGAGA