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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgcgataaatttgtgcaagtcatgttctcttgttgagatactgaaagccttaaccatttggtgttctggttttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g09000.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g09000.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G158489_T03 (Zea mays), 3'ss of exon 3
gtatgatgcgataaatttgtgcaagtcatgttctcttgttgagatactgaaagccttaaccatttg-----gtgttctggttttctatgc----agGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG
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gtatgttatgataattttcttttatttatatttacttgttgagatggttgaaattttgacttcttttccccactttttttctttgtatgcctacagGATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAG
















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|58674632|gb|CK063319.1|CK063319
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|58603054|gb|CK013582.1|CK013582
EST:     TTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|117233168|gb|CT848021.1|CT848021
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|30228290|gb|CB966181.1|CB966181
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|29640028|gb|CB645037.1|CB645037
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|58687497|gb|CK076184.1|CK076184
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|163918152|gb|EG714798.1|EG714798
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|29627838|gb|CB632849.1|CB632849
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|88395653|gb|CI590668.1|CI590668
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGAG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|27410230|gb|CA923300.1|CA923300
EST:     ACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: ACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
EST: gi|29674145|gb|CB670420.1|CB670420
EST:     TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG                         GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC
genomic: TATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTC

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: 56 (upstream exon), 67 (downstream exon)
Score: 21

CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAATATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCGgtatgatgcg ... ttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgttgagatactgaaagccttaaccatttggtgttctggttttctatgcagGATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG
                     ccttaac  putative branch site (score: 21)
                                           ttttctat  putative PPT
                                           ttttctat  TA-rich tract