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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattctactccttcctctctctccccaatccgtctgattctcgctatctgtgaacgttttggtctaatttccccccctttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC

Basic information

species Oryza sativa
transcript LOC_Os12g44000.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 1
gtattattctactccttcctctctctccccaatccgtc---tgattctcgctatctgtgaa---cgttttggtctaatttccccccc--tttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC
|||     || | ||| || |  ||      || || |    |     |||     |||     ||| | | | |   |  |    |  | | |   | | |    | |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||  ||||||| ||  | || |||||| ||| ||||||||||||||| |
gtaccgggct-cacctcccccagtccattggattcgccgctcggggagcgccccgggtgtttttcgtctcgatttggctaacaattcgatctatcccttttctcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTAC

upper sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 1
gtat-tattctactccttcctctctctccccaatc--cgtctgattctcgct--atctgtgaacgttttggtctaatttccccccctttt-------tttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC
|||  |  ||| ||||  ||     |  |  | ||  || | |     |||     | ||     ||  |  |  |||   |   |  ||       |   | | |    | ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||   | ||| |||  |||||||||| ||| |||||||||||||||||
gtacgtgctctcctcccccccaatccatcggattcgccgcccggggagcgcccaggcggttggttttccgtcccgattcggctaacaattcgatcgatcccttttcgcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC

upper sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------------gtattattctactccttcctctctctccccaatccgtctgattctcg------ctatctgtgaacgttttggtctaatttccccccctttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC
                                                       ||  | || | ||      | |  |||         || |   || |       |   ||  ||    ||  ||| || |       || |  |||||          |||| || ||||| ||||||||||||||||| ||||| ||||| |  |||||||||||||  || ||| |||| |||||  |||  ||| |||| || || |
gtctgttcctctctcctgatgtctagccctaatttttgtcatgtctttgtgatttgtggtgtttt-ctaggaaattttgctctggtgattttcaggcacttggcaagattgcttgcaaattgatttttctcatctggttgtattgtgatttgtggtgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGGCAGGTCAATCCACCCGCCGGTTTCAAACACAAAGTCACCGACAATCTTC

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|88315831|gb|CI617304.1|CI617304
EST:     CATCATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTCCCGAAAG                         GTGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG
genomic: CATCATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTCCCGAAAGgtattattct ... ctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGG




















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), 72 (downstream exon)
Score: 51

ACTCCCCTCCTTCCCGGCAGAGGAGAGGAGAGGAGAGGAGAGGACTCATCCATCATCATCAATCAACGCCATGACGAGCTCCTCATCTCCTTCCCGAAAGgtattattct ... ctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgtgaacgttttggtctaatttccccccctttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC
                gtctaat  putative branch site (score: 51)
                 tctaatttccccccct  CT-rich tract
                                tttttttttgta  TA-rich tract