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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_Os01g69130.1
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatggatgatggccagttaagctgacaatttttccttcgctaacatttctcagGTACCTTTTGAGGTCCTTGTACGCAGGCAGATCAGCAGATTGCTTGATCCAAGCCTTCAGTGTGCAGGTTTCATATACGATGAGCTAGTCAAG
                                       cgctaac  putative branch site (score: 2)
                                             catttctc  CT-rich tract
                          acaattttt  TA-rich tract