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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcgcatgcctttagctcctgaaagtcacattatgcctgaaattcttgtttgatttcgatttgtgacatacataggatataacatttcaatgcttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT

Basic information

species Oryza sativa
transcript LOC_Os07g47290.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G427620_T01 (Zea mays), 3'ss of exon 8
------------------------------------gtatgtgcgcatgcctttagctcctgaaagtcacatta------tgcctgaaattcttgtttgatttcgatttgtgacat----acataggatataacatttcaatg---cttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT
                                      ||  ||| ||| |   |  |  |    || ||| ||      | | || | |||||  ||  |||| |      | ||    | ||  |  ||  |||   ||     ||||    ||||| ||||||||||||| ||||||||| | ||||| ||| |||||||||||||||||||||||||||| |||||||||
gtatgtgtcactgttgtatataactcctttgttttttaataagcgtatgacccgatattatttgtgttacactagaaacatacatgcatttctttattcttttctagagagaaaattaaaaaatgaggcatg-catagtaacttaccttaccgttatggtcagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G080345_T01 (Zea mays), 3'ss of exon 1
------------------------------------gtatgtgcgcatgcctttagctcctgaaagtcacatta------tgcctgaaattcttgtttgattt-cgatttgtgacatacataggatataa---------catttcaatg---cttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT
                                      ||  | | ||| |   |  |  |    || ||| ||      | | || | |||||  ||  |||         || | | |||  | | ||         |||   ||     ||||    |||||| ||||||||||||  |||||||| | | ||| ||| |||||||||||||||||||||||||||| |||||||||
gtatgtgtcactgttgtatataactcctttgctttttaataagtgtatgacccgatattatttgtgttacactagaaacatacatgcatttctttattcttttatagagaaagaaaaaaataaaaaaaaatgaggcatgcatagtaacttaccttaccgttatggaaagGTTGGGACACAAATCAGTTCATGATAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 15
--------------------------------------------gtatgtgcgcatgcctttag-----ctcctgaaagtcacat-tatgcctgaaattcttgtttgatttcgatttgtgacatacataggatataacatttcaatg---cttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT
                                            |||||  |  ||    || |     | |  ||||   ||||  ||  ||  | |  ||  | ||     |    | | | | ||  |  ||  |||   ||     ||||    ||||||||||||||||||| ||||||||| | ||||| ||| |||||||||||||||||||||||||||| |||||||||
gtatgtgtcactgttgtatataactcctttgttttttaataagcgtatgacccgatattatttgtgttacactagaaacatacatgcatttctttattcttttctagagagaaaaaaataaaaaaaatgaggcatg-catagtaacttaccttaccgttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 15
----------gtatgtgcgcatgcctttagctcctgaaagtcacat-tatgcctgaaattcttgtttgatttcgatttgtgac---atacataggatataacattt-caatg-cttatata-----tatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT
           | | | |  |   | ||   |  |    |   |||  |||| |    ||||| | |  ||       |  |    ||| | || ||    |||    | |  ||||| |      ||||  |||| |||||||| ||||||||| | ||||| ||| |||||||||||||||||||||||| |||||||||||||
gtaagtgtcactgtttacataactcattgtgttatactggaagcatacatgcatctctttcttctctttttagagaaagaaaagtaataaaaagaatgaggcatgcatagtaacttatcttccccttatgagcagGCTGGGACACGGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAACTGTGGTTAAGAAT

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 12
------------------------------------gtatgtgcgcatgcctttagctcctgaaagtcacatta------tgcctgaaattcttgtttgatttcgattt-gtgacatacataggatataacattt-caatg------cttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT
                                      ||  ||| ||| |   |  |  |    || ||| ||      | | || | |||||  ||  |||| |    | || |   | |  ||    |||    | |       ||||    ||||||||||||||||||| ||||||||| | ||||| ||| |||||||||||||||||||||||||||| |||||||||
gtatgtgtcactgttgtatataactcctttgttttttaataagcgtatgacccgatattatttgtgttacactagaaacatacatgcatttctttattcttttctagagagagaaaattaaaaaatgaggcatgcatagtaacttaccttaccgttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G081682_T02 (Zea mays), 3'ss of exon 15
--------------------------------------------gtatgtgcgcatgcctttag-----ctcctgaaagtcacat-tatgcctgaaattcttgtttgatttcgatttgtgacatacataggatataacatttcaatg---cttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT-----------------------------
                                            |||||  |  ||    || |     | |  ||||   ||||  ||  ||  | |  ||  | ||     |    | | | | ||  |  ||  |||   ||     ||||    ||||||||||||||||||| ||||||||| | ||||| ||| |||||||||||||||||||||||||||| |||||||||                             
gtatgtgtcactgttgtatataactcctttgttttttaataagcgtatgacccgatattatttgtgttacactagaaacatacatgcatttctttattcttttctagagagaaaaaaataaaaaaaatgaggcatg-catagtaacttaccttaccgttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATGTGAGTGGCATGAACTAGCTCTCTCCCTT

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 16
---gta-tgtgcgcatgcctttagctcctgaaagtcacattatgcct--gaaattctt---gtttgatttcgatttgtgacatac-----ataggat-ataacatttcaatgcttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT
    || |||   |||    |    | ||  || |   | | | | |  |  ||| |    | ||||  |  ||| || | || |     ||  |||  |||| | |   || |  |  ||     ||||||||||||| ||||||||||||||||||||  | ||||| ||  ||||||||   ||||||||    |||
gtattactgtctacataaactgcttttctagaatttttacttttcttttgccattttacaggcttgacataaattagt-atattctgattatgagattgtaacctatagctgttgtttcatgaatgcagGTTGGGACACAGATCAGTTCCTTACAGATATAGCTGAGGCAACCATGGTTATGCTCAGTGTGGTCCGAAAT

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|33654092|gb|CF276706.1|CF276706
EST:     GGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: GGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29667757|gb|CB664032.1|CB664032
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29625367|gb|CB630378.1|CB630378
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29642115|gb|CB647122.1|CB647122
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29643120|gb|CB648127.1|CB648127
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|12622805|gb|AU173018.1|AU173018
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29661148|gb|CB657423.1|CB657423
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29657675|gb|CB653950.1|CB653950
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|5004160|gb|AU069309.1|AU069309
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29665147|gb|CB661422.1|CB661422
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29620969|gb|CB625980.1|CB625980
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTGCTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29644690|gb|CB649697.1|CB649697
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
EST: gi|29637954|gb|CB642963.1|CB642963
EST:     TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG                         GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA
genomic: TAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTA

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: 51 (upstream exon), 72 (downstream exon)
Score: 104

CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCGgtatgtgcgc ... atatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgatttgtgacatacataggatataacatttcaatgcttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT
                      atataac  putative branch site (score: 104)
                      atataacatttcaatg  TA-rich tract