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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGTCTTGACTCCAGACGGATCTGACCCTCAAAATCTGTGGCAAGATTGCAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatatgataaactcatgacatgtgctctactgcttcatgccttctggatgactttaccttccatccgctgtcactttggcaccttaccatctcgagaaatatttttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g74330.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74330.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G016561_T01 (Zea mays), 5'ss of exon 4
CATGTCTTGACTCCAGACGGATCTGACCCTCAAAATCTGTGGCAAGATTGCAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatatgataaactcatgacatgtgctctactgcttcatgccttctggatgactttaccttccatccgctgtcactttggcaccttaccatctcgagaa-atatttttttcag
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CATGTGTTGTCTCCAGAAGGTTCTGACCGTGAAAATCTATGGCAAAATTGCAGGATGGATATTAGCAGGTGTAGCTCAAAACAGCTTGAAGTTCTTCAAGgttgcagtggaat---cttatg---tgt-ctcttgtgtttaat------tgtgtcacttaggcctgcatc-----------ttgcaactcagtatactgaggataaggaattttcag
















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|88243001|gb|CI244123.1|CI244123
EST:     CAGAATGGATATTACCAAGTGTAATACGAGACAGCTTGAAATTCTACAAG                         GTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
genomic: CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
EST: gi|29638889|gb|CB643898.1|CB643898
EST:     CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAG                         GTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
genomic: CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
EST: gi|86413796|gb|CI068003.1|CI068003
EST:     CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAG                         GTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
genomic: CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
EST: gi|88968771|gb|CI098905.1|CI098905
EST:     ATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAG                         GTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
genomic: ATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
EST: gi|86435908|gb|CI107141.1|CI107141
EST:     TGTAATACGAAACAGCTTGAAATTCTACAAG                         GTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
genomic: TGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
EST: gi|86492818|gb|CI135451.1|CI135451
EST:     CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAG                         GTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
genomic: CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
EST: gi|29638928|gb|CB643937.1|CB643937
EST:     CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAG                         GTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
genomic: CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
EST: gi|29638888|gb|CB643897.1|CB643897
EST:     CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTATACAAG                         GTTTTAGAAAATCAATGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG
genomic: CAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGG

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: 58 (upstream exon), 18 (downstream exon)
Score: 1

CATGTCTTGACTCCAGACGGATCTGACCCTCAAAATCTGTGGCAAGATTGCAGAATGGATATTACCAAGTGTAATACGAAACAGCTTGAAATTCTACAAGgttgtaatat ... tttttttcagGTTTTAGAAAATCACTGCTTGATGCTATAAGTGAATTCAAGAAGAAAAGGGGCTGGGGCATGTTCATTGATTCATGCTTTATACATTGCCAATCCATGAA




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