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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaagccttggtccatatgatttaatcttgaaaatatagtgcttcatatgttatttgctagtaagatagaatgtctaggagtttcttatcgaat...

Basic information

species Oryza sativa
transcript LOC_Os03g36780.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G056393_T01 (Zea mays), 5'ss of exon 18
GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaagccttggtccatatgatttaatcttgaaaatatagtgcttcatatgttatttgctagtaagatagaatgtctaggagtttcttatcgaat--------
|||||| || ||||||||||||||||| |||||||| ||||||||  |||| |||||||||||||||||| |||| | | | |      | | ||  ||  |    | | | |      |||||  |   ||      | ||| | | ||  | ||   |         
GAGAAAAGGGATCATTGTTGGAAATGAGCAGGAAGGTGACGACACCATTGTAGTTTGCCATgtatgtaaatgcctggtttctt----cctgacctccaattt----tacattacccaaaatttgagaaatagtcgttttttcttgcatttcgtcatatcactaattaat
















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|88986495|gb|CI033659.1|CI033659
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|89187096|gb|CI047163.1|CI047163
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACNATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|89164137|gb|CI101225.1|CI101225
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|87027719|gb|CI274283.1|CI274283
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|86434221|gb|CI094564.1|CI094564
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|29670886|gb|CB667161.1|CB667161
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|86849356|gb|CI297811.1|CI297811
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|89192591|gb|CI049889.1|CI049889
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|88965002|gb|CI097870.1|CI097870
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|88966342|gb|CI119477.1|CI119477
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|86255945|gb|CI068394.1|CI068394
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|87023356|gb|CI272184.1|CI272184
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
EST: gi|58693580|gb|CK082267.1|CK082267
EST:     TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCAT                         GTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA
genomic: TCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACA

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), 54 (downstream exon)
Score: 13

GAGAAAGGGTATCATTGTTGGAAATGATCAGGAAGGCGACGACACAGTTGTGGTTTGCCATgtatgtaaaa ... tctctttcagGTTCCACTAAACAATATGTTTGGATATTCAACAGCTCTTCGGTCAATGACACAG




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