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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctttagatcttatcggaataaatgatggcttcatggatcatgggcaagaaattaacttttgttcttgtgcgcttactctag

Basic information

species Oryza sativa
transcript LOC_Os07g22720.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G015132_T01 (Zea mays), 5'ss of exon 17
CTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctttagatcttatcggaataaatgatggcttcatggatcatgggcaagaaattaac--ttttgttcttgtgcgcttactctag
|||||| |||||||||||||||   |||  |||| || |  || |||||||| |||||||| || ||| |||||||||| ||||||||||| |||||||  || ||  | |||     ||  | | | |   | ||||||   ||| | || |||||||     ||    |||||           
CTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt--ggtctgt---gaccacagggtta-tccatggactgtggacgaggaattaacaacgctgaaactgtgcag---------

upper sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 14
CTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctttagatcttatcggaataaatgatggcttcatggatcatgggcaagaaattaacttttgttcttgtgcgcttactctag
            ||||||||||   |||| ||||||  || ||||||||||| |||||||| || ||| |||||||||| ||||||||||| |||||||  || ||  | ||||       |    |||| || ||||||   ||| |  | |||||||| |  |  |  ||       |  ||
------------TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt--ggtctt-------tgtgcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcag
















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|86477689|gb|CI120322.1|CI120322
EST:     TGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG                         GTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
genomic: TGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctt ... cttactctagGTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
EST: gi|88955792|gb|CI092081.1|CI092081
EST:     GCAACAATGAGCTGTGATCACAGGGTTATTGATG                         GTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
genomic: GCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctt ... cttactctagGTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
EST: gi|89183783|gb|CI046348.1|CI046348
EST:     TGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG                         GTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
genomic: TGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctt ... cttactctagGTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
EST: gi|89192614|gb|CI049912.1|CI049912
EST:     TGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG                         GTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
genomic: TGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctt ... cttactctagGTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
EST: gi|88839241|gb|CI000713.1|CI000713
EST:     TGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG                         GTGCAGTCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
genomic: TGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctt ... cttactctagGTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
EST: gi|89186760|gb|CI052173.1|CI052173
EST:     TCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG                         GTGCCATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC
genomic: TCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctt ... cttactctagGTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATC

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: 72 (upstream exon), 30 (downstream exon)
Score: 11

CTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctt ... cttactctagGTGCAATCGGGGCAGAATTTCTGAAAGCATTCAAGGGCTATATCGAGAATCCAACCTCAATGTTACTGTGAAGCTAAAGATCATCAAAACTATTCTTCCC




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