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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctcctctctctctctccctctctctacctcttcgatgcggccggagatttgggttgtagaagacattttgtatgcatcgtttgcggttagatctcgaatgttaaaggaacgtcagagttccatgagcgttttgcacgatctgaagggcagtggcttgttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGGCGGCCTTCGAAGGGAACTACGCCGCATTCCACAACTACCTCATGTTGGA

Basic information

species Physcomitrella patens
transcript PP1S47_210V6.1
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|162180160|gb|FC355477.1|FC355477
EST:     AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAG                         GAATTGTGGTGATGGCAGAGGCTCA
genomic: AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAGgtgctcctct ... gttttcccagGAATTGTGGTGATGGCAGAGGCTCA
EST: gi|162190618|gb|FC366256.1|FC366256
EST:     AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAG                         GAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
genomic: AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAGgtgctcctct ... gttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
EST: gi|162157967|gb|FC334927.1|FC334927
EST:     AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAG                         GAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
genomic: AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAGgtgctcctct ... gttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
EST: gi|162229476|gb|FC404809.1|FC404809
EST:     AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAG                         GAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
genomic: AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAGgtgctcctct ... gttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
EST: gi|162160815|gb|FC336714.1|FC336714
EST:     AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAG                         GAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
genomic: AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAGgtgctcctct ... gttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
EST: gi|162196038|gb|FC372196.1|FC372196
EST:     AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAG                         GAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
genomic: AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAGgtgctcctct ... gttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
EST: gi|162168092|gb|FC343782.1|FC343782
EST:     AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAG                         GAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG
genomic: AAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAGgtgctcctct ... gttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGG

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: 25 (upstream exon), 34 (downstream exon)
Score: 3

GCGCAGTTGTATGTGAAGCAGAAAGAAGCCGATGCAGCACTCTACTCCAAAAACAAAGAAGCGGATGCAGCGCTGTACGCCAAACACAAAGAAGCTGAAGgtgctcctct ... gttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGGCGGCCTTCGAAGGGAACTACGCCGCATTCCACAACTACCTCATGTTGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagagttccatgagcgttttgcacgatctgaagggcagtggcttgttttcccagGAATTGTGGTGATGGCAGAGGCTCAAGCAGCCTACGTTAAGAGCATGCTGGCGGCCTTCGAAGGGAACTACGCCGCATTCCACAACTACCTCATGTTGGA
                                          cttgttttccc  CT-rich tract
                                           ttgtttt  TA-rich tract