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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgctttgtatcaataatttgtcagtctctgagttttctttctgtttgtcaatctgatgaagcttctatatgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAG

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G053644_T02 (Zea mays), 3'ss of exon 8
gtaattgctttgtatcaataatttgtcagtctctgagttttctttctgtttgtcaatctgatgaagcttctatatgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAG
          |  ||  || ||   |  || | | |   |||||    ||| | ||||| |||||||||||||  ||||||||||||| || |||||||| || |||||| |||||||||||||||||||  | || ||||||||||| ||||| |||||||| ||
---------gtaaatacatgataaattcgtatgtaaaacttcttat--tttctaaatcttatgaagcttctatccgattctagATGGATATATTTAACACCTTCATTGAGCTGTTACGCCAAACTGGTAATGTTACGAAAGGACAAGGCGACATCGATGAGTCCAG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 10
gtaattgctttgtatcaataatttgtcagtctctgagttttctttctgtttgtcaatctgatgaagcttctatatgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAG
          |  ||  || ||   |   | | |||   || ||    ||| | ||||| |||||||||||||  ||||||||||||| || |||||||| || |||||| |||||||||||||||||||  | || ||||||||||| ||||| |||||||| ||
---------gtaaatacatgataaattcatatgtgaaacttattat--tttctaaatcttatgaagcttctatccgattctagATGGATATATTTAACACCTTCATTGAGCTGTTACGCCAAACTGGTAATGTTACGAAAGGACAAGGCGACATCGATGAGTCCAG
















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|88353222|gb|CI654488.1|CI654488
EST:     CTTGTCCAAAGTTAATTGAATGGTTTAGGGAAAGAGAGGAAAATGTAAAG                         ATCGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
genomic: CTTGTCCAAAGTTAATCGAACGGTTTAGGGAAAGAGAGGAAAATGTAAAGgtaattgctt ... atgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
EST: gi|88307071|gb|CI640503.1|CI640503
EST:     CTTGTCCAAAGTTAATTGAATGGTTTAGGGAAAGAGAGGAAAATGTAAAG                         ATCGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
genomic: CTTGTCCAAAGTTAATCGAACGGTTTAGGGAAAGAGAGGAAAATGTAAAGgtaattgctt ... atgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
EST: gi|3106834|gb|D42559.1|D42559
EST:     CTTGT-CAAAGTTAATCGAACCGNTTAGGGAAAGAGAGGAAAATGTAAAG                         ATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
genomic: CTTGTCCAAAGTTAATCGAACGGTTTAGGGAAAGAGAGGAAAATGTAAAGgtaattgctt ... atgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
EST: gi|325494226|gb|JG458750.1|JG458750
EST:     CTTGTCCAAAGTTAATCGAACGGTTTAGGGAAAGAGAGGAAAATGTAAAG                         ATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
genomic: CTTGTCCAAAGTTAATCGAACGGTTTAGGGAAAGAGAGGAAAATGTAAAGgtaattgctt ... atgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
EST: gi|88288695|gb|CI663484.1|CI663484
EST:     CTTGTCCAAAGTTAATTGAATGGTTTAGGGAAAGAGAGGAAAATGTAAAG                         ATCGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
genomic: CTTGTCCAAAGTTAATCGAACGGTTTAGGGAAAGAGAGGAAAATGTAAAGgtaattgctt ... atgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
EST: gi|88333594|gb|CI656666.1|CI656666
EST:     CTTGTCCAAAGTTAATTGAATGGTTTAGGGAAAGAGAGGAAAATGTAAAG                         ATCGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG
genomic: CTTGTCCAAAGTTAATCGAACGGTTTAGGGAAAGAGAGGAAAATGTAAAGgtaattgctt ... atgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATG

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: 70 (upstream exon), 74 (downstream exon)
Score: 43

GCTTGTCCAAAGTTAATCGAACGGTTTAGGGAAAGAGAGGAAAATGTAAAGgtaattgctt ... atgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctctgagttttctttctgtttgtcaatctgatgaagcttctatatgattctagATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAG
                           atctgat  putative branch site (score: 43)
                                          tatatgatt  TA-rich tract