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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgcgctctctcgatgttgcagtggcgatggttgattcatgagctcaaggtgtttgcgtgtttgattgtctgatgcggtggtgttcgtctgtttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACTGTTGGGTTGGTCTGCGAGAATTACAGTGGCTTGTTCAGGCGCCCCCGTG

Basic information

species Oryza sativa
transcript LOC_Os10g35960.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G085747_T04 (Zea mays), 3'ss of exon 3
gtgagcgcgctctct-cgatgttgcagtggcgatggttgattcatgagctcaaggtgtttgcgtgtttgattgtctgatgcggtggtgttcgtctgtttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACTGTTGGGTTGGTCTGCGAGAATTACAGTGGCTTGTTCAGGCGCCCCCGTG
|||||| ||     | |  | | |   | | ||      | | ||    |   | |||    |  ||||     ||||   |||  | | || || || | | ||||| ||||||||||||||||||||||| || ||||||||||||||||| |||||||| |||||||| || |||||||| ||  ||||||| || |||||||
gtgagcccgtaggttgcagtatcgtgtttgggaaaaaaaaatgatacaatggcgatgtgcctgaatttggagtgctgacatggtaatatgcg-ctcttctcgacagGTGCTAATTGACAATATCAAGGATTTTGCCCCGATAATATACACTCCCACTGTTGGCTTGGTCTGTGAAAATTACAGCGGTCTGTTCAGACGACCCCGTG

upper sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 3
gtgagcgcgctctctcgatgttgcagtggcgatggttgattcatgagctcaaggtgtttgcgtgtttgattgtctgatgcggtggtgttcgtctgtttttg-ccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACTGTTGGGTTGGTCTGCGAGAATTACAGTGGCTTGTTCAGGCGCCCCCGTG
              | | | | |  |||| |     |   |  | | || |     |||  |  ||| |   ||| ||   |   |  |  |   || ||  ||||||||| ||||| || ||||| || || || ||||||||||||||||| || ||||| ||||| ||  | || |||   || ||||| || || || ||||
-------------gtaggtttggtggtggtgcatactagctggtaatcttagcccatttaagcatttta--atctaataaagcaatcctattgatttcttatccagGTTCTTATTGATAACATCAAAGACTTTGCACCGATAATATACACTCCCACAGTTGGATTGGTGTGTCAAAACTACTCGGGGTTGTTTAGACGTCCACGTG
















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|86821774|gb|CI309240.1|CI309240
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
EST: gi|29664101|gb|CB660376.1|CB660376
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
EST: gi|29671880|gb|CB668155.1|CB668155
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
EST: gi|29624067|gb|CB629078.1|CB629078
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
EST: gi|29656255|gb|CB652530.1|CB652530
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
EST: gi|29687359|gb|CB683634.1|CB683634
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
EST: gi|58671475|gb|CK060161.1|CK060161
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
EST: gi|58610445|gb|CK038157.1|CK038157
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCA
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCA
EST: gi|29624065|gb|CB629076.1|CB629076
EST:     GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGA                         GTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT
genomic: GGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACT

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: 74 (upstream exon), 72 (downstream exon)
Score: 54

GGAGCACAACACCCGGGGAGAGCCCGACACCATCGTCGCGCTGGCCAAGTGGAGGATCCTCAACAGGCTGCACGACCGGAACGAGACGCTGTACTACAGAgtgagcgcgc ... tttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACTGTTGGGTTGGTCTGCGAGAATTACAGTGGCTTGTTCAGGCGCCCCCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtgtttgcgtgtttgattgtctgatgcggtggtgttcgtctgtttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACTGTTGGGTTGGTCTGCGAGAATTACAGTGGCTTGTTCAGGCGCCCCCGTG
                     gtctgat  putative branch site (score: 54)
                                         tctgttttt  putative PPT
              tttgatt  TA-rich tract