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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatccttgtgtactgtttgtgttttctagactttgcacctggctgtttgagaaaacaaaataaatatatttattgaagcattaacaaagtttggtttgttctgcattgaagtaagctaattggcatgtattttatactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGGTGTGTCAAGCCAC

Basic information

species Oryza sativa
transcript LOC_Os12g42876.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 9
gtcagtatccttgtgtactgtttgtgttttctagactttgcacctggctgtttgagaaaacaaaataaatatatttattgaagcattaacaaagtttggtttgttctgcattgaagtaagctaattggcatgtattttatactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGGTGTGTCAAGCCAC
                   ||  ||| | |  |  |  | |  |||| | ||   ||   | ||  | ||| |        | ||| |    |||            ||||| || | |  | |||||| | | || ||      |||||||||||||||||||||||||||||||||||||| || |||||||| ||||||||||| || |||||||| |||||||| ||| |||| |||||||| |
-------------------gtcagtgctcttgaatccattctgctggttttt---gatgtctaagaagataaaccc-ccataccatgagtgtagtc-----------gcatttaattgactttattggcctatgttcta------cagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC

upper sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
gtcagtatccttgtgtactgtttgtgttttctagactttgcacctggctgtttgagaaaacaaaataaatatatttattgaagcattaacaaagtttggtttgttctgcattgaagtaagctaattggcatgtattttatactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGGTGTGTCAAGCCAC
                                                                                          |   |||||    |||   |    | | | |||||   ||| | |  | |     ||||||||||| ||||||||||||||||||||||||||    |||||||| ||||| | |||||||||||| || || || ||||| |||||||| |||||||
----------------------------------------------------------------------------------------gtaggatttggcagattccata----actgatctaatctacat-tgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC

upper sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ05611 (Selaginella moellendorffii), 3'ss of exon 8
gtcagtatccttgtgtactgtttgtgttttctagactttgcacctggctgtttgagaaaacaaaataaatatatttattgaagcattaacaaagtttggtttgttctgcattgaagtaagctaattggcatgtattttatactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGGTGTGTCAAGCCAC
                                                                                          |   |||||    |||   |      | | |||||   ||| | |  | |     ||||||||||| ||||||||||||||||||||||||||    |||||||| ||||| | |||||||||||| || || || ||||| |||||||| |||||||
----------------------------------------------------------------------------------------gtaggatttggcagattccatagc----tgatctaatctacat-tgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC

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|29642741|gb|CB647748.1|CB647748
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|58655717|gb|CK044397.1|CK044397
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTAGGGCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|58695495|gb|CK084182.1|CK084182
EST:     CGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: CGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|58596819|gb|CK007347.1|CK007347
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGC
EST: gi|218486915|gb|FG967742.1|FG967742
EST:     TTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: TTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|38470366|gb|CF954497.1|CF954497
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|29657694|gb|CB653969.1|CB653969
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|29619039|gb|CB624051.1|CB624051
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|58676506|gb|CK065193.1|CK065193
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|58655240|gb|CK043920.1|CK043920
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|29612828|gb|CB617841.1|CB617841
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|58680570|gb|CK069257.1|CK069257
EST:     GACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: GACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|38481553|gb|CF965642.1|CF965642
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAGACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|29638193|gb|CB643202.1|CB643202
EST:     AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
EST: gi|58611558|gb|CK039270.1|CK039270
EST:     AGATCCAGGAAGAGCTTGACATGGGTGTCCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC
genomic: AGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTC

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: 75 (upstream exon), 73 (downstream exon)
Score: 386

TGAGGAGGAGTACATCAGTGCCATCAAGGAGGAAATCAGCAAGGTTGTTAAGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... atactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGGTGTGTCAAGCCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggtttgttctgcattgaagtaagctaattggcatgtattttatactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGGTGTGTCAAGCCAC
                         agctaat  putative branch site (score: 386)
                                              tactttc  putative PPT
                                    atgtattttatacttt  TA-rich tract