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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaccattactggttcatcttctaattctagttaagattttgatgcactctgttgttaaccttccccttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGCTGTTGCTTTTGGTTCATCCTATTATCATCTCAAACCGAATGATGCCACA

Basic information

species Oryza sativa
transcript LOC_Os01g73120.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73120.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G147709_T01 (Zea mays), 3'ss of exon 2
----------gttag--accattactggttcatcttctaattctagttaagattttgatgcactctgttgttaaccttccccttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGCTGTTGCTTTTGGTTCATCCTATTATCATCTCAAACCGAATGATGCCACA
          | | |   |   |||    | ||   ||      |||   |  |   |||||||||| || ||| ||  |      || ||||||||| |||||||||||||||||||| ||||||||||||||||| || |||||||  |||||||| ||||||||||||||||| |||||||| ||||| 
gtgctgaattgctcgctgctcctaccaaatgattccctgtcctgagtcctggctc-aatgcactctgatggtaatctcgc------tgccagCTCGCAGGGGGAGCTCTGGAGTTGGACGCTGTTCTTTGCTGGTGTCACGGCTGTTGGATTTGGTTCTTCCTATTATCATCTCAACCCGAATGACGCCACC
















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|2796362|gb|AA749656.1|AA749656
EST:     GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAA                         CTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
genomic: GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAAgttagaccat ... ttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
EST: gi|29661520|gb|CB657795.1|CB657795
EST:     GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAA                         CTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
genomic: GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAAgttagaccat ... ttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
EST: gi|29668921|gb|CB665196.1|CB665196
EST:     GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAA                         CTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
genomic: GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAAgttagaccat ... ttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
EST: gi|218503174|gb|FG945918.1|FG945918
EST:     GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAA                         CTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
genomic: GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAAgttagaccat ... ttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
EST: gi|29671028|gb|CB667303.1|CB667303
EST:     GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAA                         CTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC
genomic: GGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAAgttagaccat ... ttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGC

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: 73 (upstream exon), 50 (downstream exon)
Score: 6

GGATCCCCAATACGCTGAATGTGATTTCAAACATCCCCTTCTTTTTTGTGGGTGTCGTTGGGCTCGTCTTGTGCCATTACAAAAACTACTTCAGGCTAAAgttagaccat ... ttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGCTGTTGCTTTTGGTTCATCCTATTATCATCTCAAACCGAATGATGCCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattctagttaagattttgatgcactctgttgttaaccttccccttcctggcagCTCGCAAGGGGAGCTCTGGAGTTGGACACTGTTCTTTGCTGGTGTGACTGCTGTTGCTTTTGGTTCATCCTATTATCATCTCAAACCGAATGATGCCACA
                               tgttaac  putative branch site (score: 6)
                                 ttaaccttccccttcc  CT-rich tract
         ttaagatttt  TA-rich tract