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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctgttctttggaagtttaattgcatgttttccctggccagtggccacttttttcctgttctccgtattcttaagcaaaagtttctgtatgcacattgcaatgatcctgaaaaaaagaatctggtaaattcttttcactctccctaatgatctttttatactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCTCAGTATGCGTGGGGCATCAGGGAACTCAGTTCAAGTGATTTTTGACAGC

Basic information

species Oryza sativa
transcript LOC_Os02g49800.1
intron # 4
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|66916872|gb|CX103720.1|CX103720
EST:     TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
genomic: TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
EST: gi|29618914|gb|CB623926.1|CB623926
EST:     CCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
genomic: CCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
EST: gi|27576282|gb|CA998976.1|CA998976
EST:     CACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
genomic: CACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
EST: gi|27576738|gb|CA999432.1|CA999432
EST:     TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCCAAAGGTATATTATGGGGGACCA-CAGC
genomic: TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGG-ACCAACAGC
EST: gi|27576286|gb|CA998980.1|CA998980
EST:     CACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
genomic: CACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
EST: gi|2310453|gb|C26608.1|C26608
EST:     TATNTACCCAGATGGGGAATGCCATCAACACCTATCCGGAGTGCTCCAGA                         TAACTTGTTCCACA
genomic: TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACA
EST: gi|29669337|gb|CB665612.1|CB665612
EST:     TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
genomic: TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
EST: gi|29669338|gb|CB665613.1|CB665613
EST:     ATCAACACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
genomic: ATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
EST: gi|88969944|gb|CI383446.1|CI383446
EST:     TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
genomic: TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
EST: gi|27577711|gb|CB000406.1|CB000406
EST:     CTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAA-CTTCAAAAGGTATATTATGGGGACCAACAGC
genomic: CTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGC-CCAAAAGGTATATTATGGGGACCAACAGC
EST: gi|29644454|gb|CB649461.1|CB649461
EST:     TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGA                         TAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT
genomic: TATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCT

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), 75 (downstream exon)
Score: 247

GTATCACTAGAGATCCAAATGGTGGAGGATATATGTTTCTAGGGGATGACTATGTACCCAGATGGGGAATGACATCAACACCTATCCGAAGTGCTCCAGAgtaagtcctg ... atactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCTCAGTATGCGTGGGGCATCAGGGAACTCAGTTCAAGTGATTTTTGACAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagaatctggtaaattcttttcactctccctaatgatctttttatactatcagTAACTTGTTCCACACAGAAGCCCAAAAGGTATATTATGGGGACCAACAGCTCAGTATGCGTGGGGCATCAGGGAACTCAGTTCAAGTGATTTTTGACAGC
                             ccctaat  putative branch site (score: 247)
                                      tctttttat  putative PPT
                                taatgatctttttata  TA-rich tract