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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_Os10g35960.1
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtgtttgcgtgtttgattgtctgatgcggtggtgttcgtctgtttttgccagGTTCTAATTGACAATATCAAGGATTTCGCGCCGATAATATACACTCCGACTGTTGGGTTGGTCTGCGAGAATTACAGTGGCTTGTTCAGGCGCCCCCGTG
                     gtctgat  putative branch site (score: 4)
                                         tctgttttt  putative PPT
              tttgatt  TA-rich tract