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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttttttagtttcaaacatttcactactgctgttgttcttgggatcaaagtgcggtgctgacattgaaatgctggggactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g64920.1
intron # 2
splice site 3'
intron type U2

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|88312953|gb|CI592237.1|CI592237
EST:     CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC                         ACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
genomic: CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAACgtaaggtttt ... gactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
EST: gi|88346773|gb|CI657324.1|CI657324
EST:     CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC                         ACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCCTCCGGTTGANACG
genomic: CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAACgtaaggtttt ... gactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTC-GGTTGACACG
EST: gi|88372509|gb|CI610832.1|CI610832
EST:     CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC                         ACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
genomic: CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAACgtaaggtttt ... gactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
EST: gi|300215704|gb|HO088330.1|HO088330
EST:     CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC                         ACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
genomic: CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAACgtaaggtttt ... gactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
EST: gi|87009560|gb|CI309081.1|CI309081
EST:     CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC                         ACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
genomic: CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAACgtaaggtttt ... gactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
EST: gi|29687390|gb|CB683665.1|CB683665
EST:     CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC                         ACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG
genomic: CTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAACgtaaggtttt ... gactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGG

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: 59 (upstream exon), 65 (downstream exon)
Score: 14

GCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAACgtaaggtttt ... gactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttcttgggatcaaagtgcggtgctgacattgaaatgctggggactgtgcagACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAG
                        tgctgac  putative branch site (score: 14)
                               attgaaat  TA-rich tract