Sequence
atgc intronic sequence ATGC exonic sequence...tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g46310.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069198_T05 (Zea mays), 3'ss of exon 6
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
| | || | | | | ||| | | || | |||| || ||| || || || || | || | |||| | || ||||| |||||||||||||||||||||| | |||||||| || | |||||| || |||||||||||||| |||||||||||||||||||| ||||| | || || ||
tgtctgtcaaactagcagatcacacaaccgattcttttagctttatgttgaattctccagtaatttcttatcaactaagatggcggtttactctttgtagTAATTGGAACTGCTTTTGCTCTAAACATGCTGTTCAGAATCCCAGTATGGTGTGGTGTTCTAATAACTGGACTCAGCACTCTAATGCTCTTATTGCTGCA
upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069198_T04 (Zea mays), 3'ss of exon 6
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA----------
|| |||| || ||| || || || || | || | |||| | || ||||| |||||||||||||||||||||| | |||||||| || | |||||| || |||||||||||||| |||||||||||||||||||| ||||| | || || ||
------------------------------------ta-gctttatgttgaattctccagtaatttcttatcaactaagatggcggtttactctttgtagtaattggaactgcttttgctctaaacatgctgttcagAATCCCAGTATGGTGTGGTGTTCTAATAACTGGACTCAGCACTCTAATGCTCTTATTGCTGCAGCAATATGGG
upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 5
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctcca-tggttgcttgttctttt-cagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
| | ||| ||| | | | | || | | | | ||| | || | |||| | | | | | | || |||| | | |||||||||| || || ||||| |||||||||||||| || || ||||| ||| ||||||||| | || ||||||||||| |||| || | | ||||
--ctagtttttaaaacaaaccataactttccatttcttttttctgcattctctttaacttctatttatcttaatcttgaaattttttattgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA
upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G44710.1 (Glycine max), 3'ss of exon 4
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgc--ttgttctttt-cagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
| | ||| |||| || | | || | | | | ||| | || | ||| | | | | || || |||| | | |||||||||| || || ||||| |||||||||||||| || || ||||| ||| ||||||||| | || ||||||||||| ||||||| | | | ||
--ctaggttttaaaacaaacataac-tttccatttcttttttctgcattctctttaacttttatttatcttaatcttgaatttttttcattgtacacatacagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATGCTCTTAGCATTGCA
upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 6
tttgtgatagggaaaataacaagacatctgca--actatatgcttcatattgcatctacccactat--acctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
| || | || | || ||| || | ||| ||| || | ||| || | ||||| | | | | || || || | ||| |||| |||||||| || ||||| |||||||||||||| || || |||||||||||||||||||| | || || || || || || | || || ||||
-taatggtttcttaagtg-catcctctcttcattattattaacttgatgtgtcatgcacatttcttcaacctattctgatttc-tgcatgttt-ctttttccagTGATTGGAACAGCCTTTGCATTGAACATGCTCTTCAATATTCCTGTGTGGTGTGGTGTTCTTCTTACAGGGCTTAGTACATTGGTTCTTCTAGCTTTACAMapped 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|33653430|gb|CF276044.1|CF276044EST: ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAG TAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAA-TCCCTG
genomic: ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAGgtaccagagt ... ttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
acctaac putative branch site (score: 2)
ttgcttgttcttttc putative PPT
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
-ttgtgat
- - - - - - aaaataa
- - - - - - - - - - - - -atctgca
- - - - - - - - - - - - - - - - - - - tgcttca
- - - - - - - - - - - - - - - - - - - - - - -tattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccagcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgctt