Sequence
atgc intronic sequence ATGC exonic sequencegtaagtacctctaatgtattcaaactacatttattcagtgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g22630.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G098174_T01 (Zea mays), 3'ss of exon 6
gtaagtacctctaatgtattcaaactacatt-tattcagtgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
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gtgagtatct---atttattgaacattgataacatttatcatgctcgaaggctaacaattgaaaatttttatt--atgtttatcagGTCAATGGTAGTGGGCACTTCTGTGGCATGGCTGAGATGGTCGGACCTGTTGATTTTCACAAGGACATGGACTTCTGGTGTCAGGATAAATGGACCGGAT
upper sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G056573_T01 (Zea mays), 3'ss of exon 6
gtaagtacctctaatgtattcaaactacatttattcagtgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
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gtgagtat---tgatttattgaacatccataaaatttatcatgcttaaagttcaacaattgacttt---ttttaatgtttatcagGTGAATGGGAGTGGGCACTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCACAAGGACATGGACTTCTGGTGTCAGGATAAATGGACCGGCT
upper sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G04270.1 (Glycine max), 3'ss of exon 2
----------------------------------------------gtaagtacctctaat----gtattcaaact-acatttattcag-----tgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
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gtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaacttatgtgcatctggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
upper sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G36110.1 (Glycine max), 3'ss of exon 6
-------------------------------------------gtaagtacct--ctaatgtattcaaactacatttattcag-----tgttgtctgtgattaaaatattaattctgggatttcttgtttat-cagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
||| | || || ||| || | || | | ||| |||| | | | || | ||| || | || |||| |||| ||||| | || ||||| | ||||||||| |||| |||||||| || |||||||||||||||||||| || |||||||||| ||| |
gtgagtttacattatgatgattcattcaatgagttttgattctgtattttactgatctgcatacctaaattatgtgcatctggaaatttcccttctatgatcatgctgacattttttcccttttttttcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCTGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
upper sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtacctctaatgtattcaaactacatttattcagtgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
|| ||| || ||| || | || | |||| |||| |||| | | | || | || || | |||| |||| ||||| | ||||||||||||||||||||| |||||| ||| |||| |||| |||||||| |||||| || || ||||||| ||| |
gtgagtttttcc------ttctctctttttacatgctagcttgtttgtg-ttaagcttattctgatgcattgcttttctttttagGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
upper sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtaa-gtacctctaatgtattcaaa-ctacatttattcagtgttgtctgt--gattaaaata------ttaattctgggatttcttgtttat-cagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
||| | | || | | || ||| |||| | | ||| ||| |||| | | | || || || || || || ||||| |||| || || | |||||||| | || |||||| |||| ||||||||||| |||||||| |||||||| ||| || ||||| |||| ||| |
gtgagttttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAAMapped 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|568784|gb|D39633.1|D39633EST: GGATAGCTAAGAGGAATTCTACCAAGTGCCCTGTTTTTCTGTTCTTCTCC GTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGA
genomic: GGATAGCTAAGAGGAATTCTACCAAGTGCCCTGTTTTTCTGTTCTTCTCCgtaagtacct ... tgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGA
EST:
gi|218505169|gb|FG956729.1|FG956729EST: GAATTCTACCAAGTGCCCTGTTTTTCTGTTCTTCTCC GTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTT
genomic: GAATTCTACCAAGTGCCCTGTTTTTCTGTTCTTCTCCgtaagtacct ... tgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattcagtgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
tattaat putative branch site (score: 2)
tttcttgttt putative PPT
tctgtgattaaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtacctctaatgtattcaaactacatttattcagtgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA