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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttaatgcaaaaagcatattttcaaaccatcattactactttggcatgcacgctgtctattttgcgaaggctcgcctcatgatatcctttgaaggagtttgcaaagtatgtattctacttccgaacatgtgactccgctgattttgaggcatgtcttgggcagGTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAACTTTGTTCAAAGCATTCTGGCATCACACGGACGCTATCTTGTGCTGTGCA

Basic information

species Physcomitrella patens
transcript PP1S67_107V6.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S67_107V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: EFJ29546 (Selaginella moellendorffii), 3'ss of exon 15
gtgttaatgcaaaaagcatattttcaaaccatcattactactttggcatgcacgctgtctattttgcgaaggctcgcctcatgatatcctttgaaggagtttgcaaagtatgtattctacttccgaacatgtgactccgctgattttgaggcatgtcttgggcagGTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAACTTTGTTCAAAGCATTCTGGCATCACACGGACGCTATCTTGTGCTGTGCA------
                                                                                                               |||      ||  | |    ||  |  | |    || ||  |    | | |||||    |||| |    |||||||||   ||| ||    ||| |   |||  ||||            ||||||||||| |||||||||| |||||||| |       
---------------------------------------------------------------------------------------------------------------gtaaagc-tttttgtatccttggtt--gatatcattaagcaaccgatcgtgcagGGCAAACTTCGCCTCGGATCTCACTGAGTCGGATCCAGGAAGCACTGACGCTTT------------CTGGCATCACAAGGACGCTATCCTGTGCTGTACCTGGAAG

upper sequence: PP1S67_107V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: EFJ38766 (Selaginella moellendorffii), 3'ss of exon 15
gtgttaatgcaaaaagcatattttcaaaccatcattactactttggcatgcacgctgtctattttgcgaaggctcgcctcatgatatcctttgaaggagtttgcaaagtatgtattctacttccgaacatgtgactccgctgattttgaggcatgtcttgggcagGTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAACTTTGTTCAAAGCATTCTGGCATCACACGGACGCTATCTTGTGCTGTGCA------
                                                                                                               |||      ||  | |    ||  |  | |    || ||  |    |   |||||    |||| |    |||||||||   ||| ||    ||| |   |||  ||||            ||||||||||| |||||||||| |||||||| |       
---------------------------------------------------------------------------------------------------------------gtaaagc-tttttgtatccttggtt--gatatcattaagcaaccgatcatgcagGGCAAACTTCGCCTCGGATCTCACTGAGTCGGATCCAGGAAGCACTGACGCTTT------------CTGGCATCACAAGGACGCTATCCTGTGCTGTACCTGGAAG
















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|162184098|gb|FC358844.1|FC358844
EST:     AATCCAGACGCACTTTCCTTAGCACGTCATGTCNTTAGGAGCTACAG                         GTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAAC
genomic: AATCCAGACGCGCTTTCCTTAGCACGTCATGTCCTTAGGAGCTACAGgtgttaatgc ... tcttgggcagGTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAAC
EST: gi|162204058|gb|FC379427.1|FC379427
EST:     GCTAATCCAGACGCACTTTCCTTAGCACGTCATGTCCTTAGGAGCTACAG                         GTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAAC
genomic: GCTAATCCAGACGCGCTTTCCTTAGCACGTCATGTCCTTAGGAGCTACAGgtgttaatgc ... tcttgggcagGTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAAC

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: 33 (upstream exon), 32 (downstream exon)
Score: 13

CGATGGCTTTAGCCCCGTCCCGAGGATCTGCTCCGCCCCGTCAAATGTCTGCTAATCCAGACGCGCTTTCCTTAGCACGTCATGTCCTTAGGAGCTACAGgtgttaatgc ... tcttgggcagGTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAACTTTGTTCAAAGCATTCTGGCATCACACGGACGCTATCTTGTGCTGTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtattctacttccgaacatgtgactccgctgattttgaggcatgtcttgggcagGTTGCACTTGGGTCTGGATCTCACGAGGTCAGAAAACGGAGGAGATGAAACTTTGTTCAAAGCATTCTGGCATCACACGGACGCTATCTTGTGCTGTGCA
                           cgctgat  putative branch site (score: 13)
                              tgatttt  TA-rich tract