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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatttggccaaagtagttatttctttgaaaaaaaaagtgatcctggctgttcctgagttttagcttttatttcattgattcaagttcattatagtatgcccttttcagcccttaagttccatcgatttcataaaatactgttgaacatctcatgggagcatagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG

Basic information

species Oryza sativa
transcript LOC_Os10g31830.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g31830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G075051_T01 (Zea mays), 3'ss of exon 4
gtactatttggccaaagtagttatttctttgaaaaaaaaagtgatcctggctgttcctgagttttagcttttatttcattgattcaagttcattatagtatgcccttttcagcccttaagttccatcgatttcataaaatactgttga-acatctcatgggagc-atagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG
                                                                                              | | | ||   || | |    | ||  |  || | || | ||    |   |    |||  || |     | |||  |||||||||||     |||||  |||| ||||||||||  ||||||| ||| ||||| ||||| ||||| ||||||| |||||| || ||||||||||| || || ||||||||||| || ||||
----------------------------------------------------------------------------------------------acattctgaagttctaaaaagtaaaactg-atgggttccttaggggagaataactacagttcctacttcctatatctgattttgatgtcctcatcttgtagGATGATGAAAGAATGGTCACAAAAGAGGAAGGTCTTGCTTTTGCTGAAGAATATGGATGTCTGTTTCTTGAGAGCAGTGCAAAAACACGAGAAAACGTTG

upper sequence: LOC_Os10g31830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G809265_T02 (Zea mays), 3'ss of exon 4
gtactatttggccaaagtagttatttctttgaaaaaaaaagtgatcctggctgttcctgagttttagcttttatttcattgattcaagttcattatagtatgcccttttcagcccttaagttccatcgatttcataaaatactgttga-acatctcatgggagc-atagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG
                                                                                              | | | ||   || | |    | ||  |   | |  |   |||  ||   |    |||  ||||     | ||   |||||||||||||   ||||| ||||| ||||||||||  ||||||  ||||||||| ||||| ||||| ||||||||||| || || ||||||||||| || || ||||||||||| |||||||
----------------------------------------------------------------------------------------------acattctggagttgtaaaaagtcaaactg-gtgggctctttaaggtagaataactacagttcatacttcctatttctgattttgatggtctcatcttgcagGATGATGAAAGAATGGTCACAGAAGAAGAAGGTCTTGCTTTTGCTGAAGAATCTGGTTGTCTGTTTCTTGAGAGCAGTGCAAAAACACGAGAAAATGTTG
















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|88257675|gb|CI360261.1|CI360261
EST:     CATCAAACAAAGACTGCAT-AAAATGCTTGTT-GAAACAAAATTGACAAG                         GAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTGGCAGAAGAA
genomic: CATCAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAATTGACAAGgtactatttg ... tatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAA
EST: gi|86869456|gb|CI346316.1|CI346316
EST:     CATCAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAATTGACAAG                         GAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAA
genomic: CATCAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAATTGACAAGgtactatttg ... tatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAA
EST: gi|88273405|gb|CI393811.1|CI393811
EST:     GCATAAAAATGC-TGTT-GAAACAAAATTGACAAG                         GAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAA
genomic: GCATAAAAATGCTTGTTGGAAACAAAATTGACAAGgtactatttg ... tatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAA

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: 66 (upstream exon), 67 (downstream exon)
Score: 13

AAGCTTCACAAATCTGGCTGAAGTATGGAGTAAGGAAATAGAGTCACACTCATCAAACAAAGACTGCATAAAAATGCTTGTTGGAAACAAAATTGACAAGgtactatttg ... tatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactgttgaacatctcatgggagcatagttgattttgatggttctatctttcagGAGGATGAAAGAACTGTCACAAGAGAAGAAGGGCTTGCCTTTGCAGAAGAATCTGGATGCCTATTTCTTGAGAGTAGCGCGAAAACACGAGATAATGTTG
                                 ttttgat  putative branch site (score: 13)
                                          ttctatctttc  putative PPT
                             ttgatttt  TA-rich tract