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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctctaactatggttacttcacatttaacctcatatttctttgccttaaataattttgctttcagcctatcatacagttatgtcctaaaccatgtaaataattctttcgcgttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAACTGGACGATCCCCCCGTTAGTGACTCCCTGCACATCGAGGTCCTGAGCA

Basic information

species Physcomitrella patens
transcript PP1S9_391V6.1
intron # 11
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|37843998|gb|BJ602006.1|BJ602006
EST:     CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCG                         GTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
genomic: CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCGgtaagctcta ... gttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
EST: gi|162274566|gb|FC451009.1|FC451009
EST:     CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCG                         GTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
genomic: CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCGgtaagctcta ... gttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
EST: gi|162269310|gb|FC444801.1|FC444801
EST:     CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCG                         GTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
genomic: CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCGgtaagctcta ... gttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
EST: gi|162267809|gb|FC443799.1|FC443799
EST:     CAAACCCCTTTGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCG                         GTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
genomic: CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCGgtaagctcta ... gttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
EST: gi|18334682|gb|BJ166699.1|BJ166699
EST:     CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCG                         GTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
genomic: CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCGgtaagctcta ... gttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
EST: gi|162269311|gb|FC444802.1|FC444802
EST:     CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCG                         GTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA
genomic: CAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCGgtaagctcta ... gttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAA

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: 35 (upstream exon), 35 (downstream exon)
Score: 40

GCTGTCGGTCATCATTCATCAGGCCCAGGAATTAGAAGGCAAACATCACACAAACCCCTTCGTGGAGGTTAATTTTCGGGGGGATAAAAAGAAAACTCCGgtaagctcta ... gttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAACTGGACGATCCCCCCGTTAGTGACTCCCTGCACATCGAGGTCCTGAGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatcatacagttatgtcctaaaccatgtaaataattctttcgcgttcctttagGTTGTGAAGAAAAATAAAAACCCCAGATGGGATCAACTATTTACTTGGCAACTGGACGATCCCCCCGTTAGTGACTCCCTGCACATCGAGGTCCTGAGCA
                 tcctaaa  putative branch site (score: 40)
                                    ttctttcgcgttcctt  putative PPT
                          atgtaaataattcttt  TA-rich tract