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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtaacgcctccccccgcccccagatttcccccccctttcccccaatcttcgagttcccctgcggcgtggtggctggatcgctcagatctgagccgggttgcaatgccggattgtttgggagggtttctgacgctgttgccgtggtgaatcgcgggtgtgggtgtgggtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGTGACATTGGCCGCCTCTTCATCGCCGGCTTCGGCTC

Basic information

species Oryza sativa
transcript LOC_Os10g37520.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 1
gtgcgtaacgcctccccccgcccccagatttcccccccctttcccccaatcttcgagttcccctgcggcgtggtggctggatcgctcagatctgagccgggt-tgcaatgccggattgtttgggagggtttctgacgctgttgccgtggtgaatcgcgggtgtgggtgtgggtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGTGACATTGGCCGCCTCTTCATCGCCGGCTTCGGCTC
    |||    | || || |   || | ||   |||| |  || |||   ||   | | ||  |||| || ||   |||   |   ||||||||  | |||   |||||||||| | || |  |  ||| |  | | |||  |   | |||   ||     | || ||        |||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||
----gta----cgcctcctgattcctgcttggtcccctccctcgcccttcctcgcattcccgttgcgtcgcggca-ctgcgccctccagatctggactgggggcgcaatgccgg-tggtatttggtggtctg-gtctctgacgttattgtgctccg-----gcggatgg-------tgcagCTGGGGACTGGCTGCAGGGGCCCTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGCGACATTGGCCGCCTCTTCATCGCCGGCTTCGGTTC

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 1
gtgcgtaacgcctccccccgcccccagatttcccccccctttcccccaatcttcgagttcccctgcggcgtggtggctggatcgctcagatctgagccgggttgca-atgccggattgtttgggagggtttctgacgctgttgccgtggtgaatcgcgggtgtgggtgtgggtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGTGACATTGGCCGCCTCTTCATCGCCGGCTTCGGCTC
                                                                                |||  | ||| ||| |  | |||| | ||    |   | || |     ||  |||  |  ||    |   |     | | | |   ||   ||      ||||||||| ||| ||||||| || || ||||||||||||||||| || || || |  |  ||||| |||||||| |   | || || || || || || ||
--------------------------------------------------------------------------------atcattaagaactg-gttgagttgaatataattgtggggttagcttctttcttgattccatttttttaaggttgtactgatttatttgattgtggcaatagCTGGGGACTGGTTGCAGGGTCCTTATGTGTACTACCTCTACAGTCAATATGGTTATGGGAAGGGGGACATTGGGCAATTGTTTATTGCTGGTTTTGGGTC

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 1
gtgcgtaacgcctccccccgcccccagatttcccccccctttcccccaatcttcgagttcccctgcggcgtggtggctggatcgctcagatctgagccgggttgcaatgccggattgtttgggagggtttctgacgctgttgccgtggtgaatcgcgggtgtgggtgtgggtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGTGACATTGGCCGCCTCTTCATCGCCGGCTTCGGCTC
                                         |       |  |||| ||| || ||   | | ||  |  | | |  ||||||  |||   | ||     |||||   | |       |  | || || || ||    |    | |                |    |||| || |||||||| ||||| || ||||| |||| |||||||||||| || |||||| | ||||| || ||||| || ||||||||||| ||||| || ||
----------------------------------------gtgagttctttctcgatttcgcccgcattgcg-tgcttccagctcctagatctc-gccaaat-gcgtactcggatctctaga------tcttaactctcttccctctttcttcctc----------------tcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ21113 (Selaginella moellendorffii), 3'ss of exon 1
gtgcgtaacgcctccccccgcccccagatttcccccccctttcccccaatcttcgagttcccctgcggcgtggtggctggatcgctcagatctgagccgggttgcaatgccggattgtttgggagggtttctgacgctgttgccgtggtgaatcgcgggtgtgggtgtgggtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGTGACATTGGCCGCCTCTTCATCGCCGGCTTCGGCTC
                                         |       |  |||| ||| || ||   | | ||  |  | | |  ||||||   |      ||| |  |||||   | |       |  | || || ||  |    |   || |                |    |||| || |||||||| ||||| || ||||| |||| |||||||||||| || |||||| | ||||| || ||||| || ||||||||||| ||||| || ||
----------------------------------------gtgagttctttctcgatttcgcccgcattgcg-tgcttccagctcctagatctcgccaaatgcgcact--cggatctctaga------tcttaactctcttctctctttctttctc----------------tcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC

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|88825289|gb|CI775854.1|CI775854
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|88388856|gb|CI592744.1|CI592744
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|88415269|gb|CI586475.1|CI586475
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|88402489|gb|CI596350.1|CI596350
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|88361351|gb|CI626455.1|CI626455
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|58609294|gb|CK037327.1|CK037327
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|88734539|gb|CI758047.1|CI758047
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|7134673|gb|AU082615.1|AU082615
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|58675854|gb|CK064541.1|CK064541
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGTTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|88718568|gb|CI742078.1|CI742078
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|58694444|gb|CK083131.1|CK083131
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGTTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|86888184|gb|CI301876.1|CI301876
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
EST: gi|88764709|gb|CI773827.1|CI773827
EST:     CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGT                         CTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG
genomic: CTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACG

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: 72 (upstream exon), 10 (downstream exon)
Score: 3

GGGCTGGAGCTCGGCAAGTCCGGCAAGGACCGCGTCGCCACCACCCCGGCCTTCAACGCGTTCAAGAACAACTACATCCTCGTCTACTCGCTCATGATGTgtgcgtaacg ... gtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGTGACATTGGCCGCCTCTTCATCGCCGGCTTCGGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttctgacgctgttgccgtggtgaatcgcgggtgtgggtgtgggtttttgcagCTGGGGATTGGCTGCAGGGGCCGTACGTGTACTACCTCTACAGCCAGTACGGCTTCGACAAGGGTGACATTGGCCGCCTCTTCATCGCCGGCTTCGGCTC
   ttctgac  putative branch site (score: 3)
                                              tttttgc  putative PPT
                                              ttttt  TA-rich tract