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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTTCTCTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagccagagattactttcactgtctttttctcttcaccatcaatagaacacctgttaactgaatgcatactgtcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g10340.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G871861_T02 (Zea mays), 5'ss of exon 9
AAACTTCTCTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagccagagattactttcactgtctttttctcttcaccatcaatagaacacctgttaactgaa-tgcatactgtcgcag
|||||||| |||||||| || || || ||||| ||| |||||| ||||||||| |  |||||||||||||||||| |||||| ||||| ||||| ||||| |||| |   ||||  |||| |   || | ||| ||||| |||
AAACTTCTTTGCCAGCATTTTGATCTCGACAGACGATTGATTGGATACCTATCCACCTgtaagtcagccagagatgactttcgctgtccttttcacttcatcatctacgtaacatatgttgatcaaaatacatcctgtcacag
















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|88296579|gb|CI537546.1|CI537546
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTTTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|88374674|gb|CI518541.1|CI518541
EST:     CTGCCAGCACTTCGACCTTGACGGGCGACTGATTGAATACCTATTTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|14713541|gb|AU197539.1|AU197539
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|86845834|gb|CI347093.1|CI347093
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|572096|gb|D41607.1|D41607
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|88506530|gb|CI434036.1|CI434036
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATGTAGAT                         GACCCATCATCTATCCCAGCTGTCTCGAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|88513134|gb|CI440640.1|CI440640
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCCATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|571728|gb|D41239.1|D41239
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGANTACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|570054|gb|D40903.1|D40903
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|86259409|gb|CI008086.1|CI008086
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|89178659|gb|CI391657.1|CI391657
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|88463250|gb|CI524560.1|CI524560
EST:     CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGAT                         GACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT
EST: gi|88304712|gb|CI520567.1|CI520567
EST:     GTGCCAGCACTTGGACCTTGACAGGCGACTGATTGGATACCTATGTAGAT                         GACCCATCATCTATCCCAGCTGTCTCGAAAAGAAAGCGCCAATTCCCTTTT
genomic: CTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTT

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: 45 (upstream exon), 13 (downstream exon)
Score: 1

AAACTTCTCTGCCAGCACTTCGACCTTGACAGGCGACTGATTGAATACCTATCTAGATgtaagtcagc ... actgtcgcagGACCCATCATCTATCCCAGCTGTCTCAAAAAGAAAGCGCCAATTCCCTTTTGTCGACGAACCAGATGAATGAACCGGACAGTTGTGCGGCAGCAATCACT




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