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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcattaataattcatgcattacggagcaaaaataattgtagccaacctaaaaggtggttgtgatttctctgtacttttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g05630.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 3
GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatg---gcattaataattcatgcattacggagcaaaaataattgta-gccaacctaaaaggtggttgtgatttctctgtacttttcttgcag
| || || ||||   |||| ||||| || || |||||||| ||||||||||||||||| || || ||||||||||||| ||||| |||| ||||||| ||||||     | |||  ||| | |  ||  |      | |      || |     ||  |       |    ||| | | |  ||||  |||||
GTCACGGAGGAGTCAGAGCAGCTGAGTACGTTAAGCAGCATCTTTTCAGCAATTTAATCAAACACCCAAAGTTCATCACTGATACCAAGGCCGCTATTGgtatgctcatactaactattgaggacttttgacttctacactgacatatgatggtcttgatatc--ctcccgtttttttttttttttgctgcag

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G829894_T02 (Zea mays), 5'ss of exon 2
GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcattaataattcatgcattacggagcaaaaataattgtagccaacctaaaaggtggttgtgatttctctgtacttttcttgcag---
| ||||| ||||  ||||| ||||| ||||| |||||||||||||||||||||||||| || || ||||||||||||| ||||| |||| | ||||||||||      || ||  | |   |||   ||      |    |  |   |    | | |||| |  ||||  |  |||| | || |||| |   
GTCATGGAGGAGTCCGAGCAGCTGAGTATGTTAAGCAGCACCTTTTCAGCAATTTAATCAAACACCCAAAGTTCATCACTGATACCAAGGCTGCTATCGgtactttcatattagcttaactattgtagacttttgacttgtacactgag---atatggtgatcttgatacccttgtattatttttgctgcag

upper sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 4
GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatg----------gcattaataattcatgcattacggagcaaaaataattgtagccaacctaaaaggtg--gttgtgatttctctgtacttttcttgcag
| ||||| || |||||||| ||||||||||| || ||  ||||||| || ||||| || | |||||||||||||||   |||||  || || ||||| ||| ||          |    | ||||     | ||    |||    || |  ||   ||  |||||   |   ||  | | || ||    || | | |||||
GTCATGGAGGTGCTCGAGCAGCTGAATATGTTAAACAAAACCTTTTTAGTAATTTGATCAGGCATCCAAAGTTCATTTCTGATACAAAATCAGCTATAGgtttgtttcctgactgtgccagtaatgt-cactttctatagcctgtatgaa-gtgttcactctaaatactactgtcttaaattatcct--ctgtacatgcag

Mapped 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|5003494|gb|AU068643.1|AU068643
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|33680351|gb|CF308590.1|CF308590
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|218495837|gb|FG960245.1|FG960245
EST:     AATTTAATTAATGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: AATTTAATTAA-GCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
EST: gi|33675133|gb|CF303372.1|CF303372
EST:     CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCG                         CTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC
genomic: CAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 85

GCCATGGCGGAGCTCGAGCGGCTGAATATGTCAAGCAGCACCTTTTCAGCAATTTAATTAAGCATCCAAAGTTCATCAGTGATATCAAGTCCGCTATCGgtatggcatt ... tttcttgcagCTGAAACGTACAACCATACAGATTCAGAATTTCTGAAAGCCGAAAGTAGTCACACTAGGGATGCTGGCTCAACTGCCTCAACAGCTATTCTTGTAGGCGA




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