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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataccatcccactttaggaagaacgattgtaagagtaattcatggatgatggccagttaagctgacaatttttccttcgctaacatttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCAAGCCTTCAGTGTGCAGGTTTCATATACGATGAGCTAGTCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g69130.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G180335_T03 (Zea mays), 3'ss of exon 2
-----gtataccatcccactttaggaagaacgattgtaagagtaattcatgg--atgatggccag----ttaagctgacaatttttccttcgctaacatttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCAAGCCTTCAGTGTGCAGGTTTCATATACGATGAGCTAGTCAAG
      |  |||  ||   | | |   | |  ||||          |||  |  || ||          || ||||||||||| ||   |  | | || ||   |||| || ||||| ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||   |||||||| ||||| || || |||
gtaagatgcacctgcctcttattgtgtgcattattgaggctcaggctcacagcaattatcattgaaacatttagctgacaattctttgctaacaatcacttaa-agGTTCCATTTGAAGTCCTTGTACGTAGGCAGATCAGCAGATTGCTTGATCCAAGTCTTCAGTGTGCACAGTTCATATATGATGAACTTGTAAAG

upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 10
-----gtataccatcccactttaggaagaacgattgtaagagtaattcatggatgatggccagttaagctgacaatttttccttcgctaacatttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCAAGCCTTCAGTGTGCAGGTTTCATATACGATGAGCTAGTCAAG
      |  |||  ||   | | |   | |  ||||    |   |   ||    | |||    || |||||| |||| ||   |  | | || ||   |||| || ||||| ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||   |||||||| ||||| || || |||
gtaagatgcacctgcctcttattgcgtgcattattgaggcacatagcaatcatcgttggaacttttagctgataattctttgctaacaatcacttaa-agGTTCCATTTGAAGTCCTTGTACGTAGGCAGATCAGCAGATTGCTTGATCCAAGTCTTCAGTGTGCACAATTCATATATGATGAACTTGTAAAG
















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|58672080|gb|CK060766.1|CK060766
EST:     TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG                         GTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
genomic: TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAGgtataccatc ... catttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
EST: gi|58679026|gb|CK067713.1|CK067713
EST:     TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG                         GTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
genomic: TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAGgtataccatc ... catttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
EST: gi|58658952|gb|CK047632.1|CK047632
EST:     TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG                         GTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
genomic: TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAGgtataccatc ... catttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
EST: gi|58695675|gb|CK084362.1|CK084362
EST:     TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG                         GTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
genomic: TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAGgtataccatc ... catttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
EST: gi|66928093|gb|CX114941.1|CX114941
EST:     TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG                         GTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA
genomic: TGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAGgtataccatc ... catttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCA

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), 65 (downstream exon)
Score: 18

GATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAGgtataccatc ... catttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCAAGCCTTCAGTGTGCAGGTTTCATATACGATGAGCTAGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatggatgatggccagttaagctgacaatttttccttcgctaacatttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCAAGCCTTCAGTGTGCAGGTTTCATATACGATGAGCTAGTCAAG
                                       cgctaac  putative branch site (score: 18)
                                             catttctc  CT-rich tract
                          acaattttt  TA-rich tract