Sequence
atgc intronic sequence ATGC exonic sequence...tgattgaatctgttaaggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g36740.5 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 1
tgattgaatctgttaa--ggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
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--gtctaaccgcctacctaagtttgtcttttaccatcctgtatgtgcaaaccattgcataaatctgtttgctaattttgttatactacatctgttcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G118957_T04 (Zea mays), 3'ss of exon 3
tgattgaatctgttaa--ggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
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--gtctaactgcttacctaagtttgtcttttgccatcctgtacgagccaagcattgcataaatctgtttgctaatttttttataccacatttgtttgcacagTATGCTCACAGGGAATGTGTGCAACGTTGGTGCAATGAGAAAGGAGATATAATCTGTGAAATCTGCCATGAG
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G04870.1 (Glycine max), 3'ss of exon 1
tgattgaatctgttaaggattttttttttgttttactgtatttcttt---tgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
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--gagacatct-ttgttttttttttttttcctttaatatgcttgcttgcatttctattttgtgttaataatgatttgtggttttttggaaattttacgtacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAACTTGTGAGATATGTCACAAG
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G35750.2 (Glycine max), 3'ss of exon 1
-tgattgaatctgttaaggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagat-tttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
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tttatgtggcatcttt--gttttttttttttttttcttttaatatgcttgcatttccattttgtgttaacgattggtgattttttggaaatttcatgaacagTATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAG
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
tgattgaatctgttaaggattttttttttgt-tttactgtatt--tcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
| | | | | || | | |||| ||| || | |||| | | | ||| | ||| | | ||| | | | | |||| |||||||| ||||||| ||| |||||||||||||||||||||| ||| || || ||||| || |
acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctaga---ctagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
upper sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 3'ss of exon 4
tg-attgaatctgttaag-gattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagat-tttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
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tgtattgtcattatgagataaaatttagtactccttgatatttttctctctaactccat---tgtcagtcaaatttgttattgactgtatattttttttccagTATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGMapped 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: CGCTTGTAGCGGTTAGCCTCAAG TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
genomic: CGCTTGTAGCGG-TAGCCTCAAGgtatgttgtt ... tattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
EST:
gi|29677125|gb|CB673400.1|CB673400EST: TAGCGGTAGCCTCAAG TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
genomic: TAGCGGTAGCCTCAAGgtatgttgtt ... tattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
ttttgat putative branch site (score: 4)
ttttatt putative PPT
tatatttctacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgattgaatctgttaaggattttttttttgttttactgtatttcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA