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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAAAAGTTGCTGATTTTGGTCTCTCTCGGCTTGCCCCAGAGCCAGAATCAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagctatgccatctgtttgtacatgctctgtgagcaactagttgagcagaagtctgccacatttgccagcacttttatcagtttttacttcagtt...

Basic information

species Oryza sativa
transcript LOC_Os01g72990.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72990.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G165597_T01 (Zea mays), 5'ss of exon 10
CGCAAAAGTTGCTGATTTTGGTCTCTCTCGGCTTGCCCCAGAGCCAGAATCAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagctatgccatctgtttgtacatgctctgtgagcaactagttgagcagaagtctgccacatttgccagcacttttatcagtttttacttcagtt
|||||| ||||||||||| |||||||| || ||||| ||   ||||||| ||||||||| ||| ||||||||||| || || ||  |||| || |||||||| |||| ||  |  |  |  ||     ||       ||||   || | |    |   || |    || |   |   || ||                  
CGCAAAGGTTGCTGATTTCGGTCTCTCACGCCTTGCTCCGCTGCCAGAAACAGAGGGGAGTGCCCCTGGTCATGTCTCCACAGTCGTAAAAGGCACCCCGgtaagtacctcagatacatacttactggtg------aagcacacagatcaattcatacctcctctcttggttggtttttgtag-----------------

upper sequence: LOC_Os01g72990.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA11G31510.1 (Glycine max), 5'ss of exon 17
CGCAAAAGTTGCTGATTTTGGTCTCTCTCGGCTTGCCCCAGAGCCAGAATCAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagctatgccatctgtttgtacatgctctgtgagcaactagttgagcagaagtctgccacatttgccagcacttttat-cagtttttacttcagtt---
||| ||||| ||||||||||| ||||| |||||||||||||  |||||    || ||  |||  ||||||||||| || || ||  ||||||| |||||||| ||  ||| |      || || |   |   |||  |      | |||   |  |   | | | ||| || | ||  ||  | || |  | ||| || |    
CGCGAAAGTGGCTGATTTTGGACTCTCACGGCTTGCCCCAGTTCCAGACATGGAAGGAGTTGTGCCTGGTCATGTATCTACAGTGGTAAAGGGGACCCCGgtaag--gctttcatgattggttttggttttgctg-aattgtgcacttgtatattaag-tacaagattggcaatcatattgttgcaatactaactgcactagtt

upper sequence: LOC_Os01g72990.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv08s0056g00570.t01 (Vitis vinifera), 5'ss of exon 34
CGCAAAAGTTGCTGATTTTGGTCTCTCTCGGCTTGCCCCAGAGCCAGAATCAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagta--gctatgccatc-tgtttgtacatgctctgtgagcaacta-gt-tgagcagaagtctgccacatttg---ccagcacttt-tatcagtttttacttcagtt--------------------------------------------------------------------------------
  | ||||||||||||||||| ||||| |||||||| ||||| | ||||   || |||  ||  |||  |||||| || ||  || | ||||| || ||||| || |   ||     | | |  |   | |||    |   |   | | || ||| |    |  |   | | | |     ||  |    |   ||||   | || | ||                                                                                
ACCTAAAGTTGCTGATTTTGGACTCTCACGGCTTGCACCAGACCTAGAAGATGAAGGGGCTGTGCCTAATCATGTATCCACCATTGTGAAGGGAACACCGgtaagcatgacttcattaacatcatcaaatatgtaaggcaggtccccatgtatgatcgagtggattggaaactagggtttagtgcccaatgagagttcccatttaacttcactgttctcattaaatagcatatgacagtaattatttttattcatgtgataactctcttgatggatgatctacctgcag

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|29658490|gb|CB654765.1|CB654765
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29624083|gb|CB629094.1|CB629094
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTGTAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29681602|gb|CB677877.1|CB677877
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29659291|gb|CB655566.1|CB655566
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAANAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29659292|gb|CB655567.1|CB655567
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29659458|gb|CB655733.1|CB655733
EST:     CAGAGAGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|86502307|gb|CI144940.1|CI144940
EST:     GGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: GGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29658489|gb|CB654764.1|CB654764
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29660411|gb|CB656686.1|CB656686
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29678739|gb|CB675014.1|CB675014
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29657729|gb|CB654004.1|CB654004
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29666345|gb|CB662620.1|CB662620
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTAGTCATAAGCTGACAGCCAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
EST: gi|29627357|gb|CB632368.1|CB632368
EST:     CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTGTAAAGGGTACCCCG                         GGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT
genomic: CAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGT

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: 64 (upstream exon), 50 (downstream exon)
Score: 9

CGCAAAAGTTGCTGATTTTGGTCTCTCTCGGCTTGCCCCAGAGCCAGAATCAGAGGGGATTGCTCCTGGTCATGTGTCAACTGTTATAAAGGGTACCCCGgtgagtagct ... acaatcgcagGGTTATCTTGATCCGGAGTATTTCCTTACTCATAAGCTGACAGACAAAAGTGACGTGTACAGCCTTGGTGTTGTTTTTCTGGAACTGCTGACAGGGATGC




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