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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcacctttaccattttccttataactatcacatagctgcgaggaattgtaatagtgatcgttgattgaaaactgagtcttgtgccttcttcgtgagcagGAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCAACGGCTTCGGCCGCTTCGGTCGTTTGGTTGCTAGAGTCGCTCTAGAGAG

Basic information

species Physcomitrella patens
transcript PP1S9_47V6.1
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|100354749|gb|BY983546.1|BY983546
EST:     TCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAG                         GAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCA
genomic: TCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAGgtattgctcc ... tcgtgagcagGAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCA
EST: gi|100441025|gb|BY962513.1|BY962513
EST:     TCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAG                         GAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCA
genomic: TCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAGgtattgctcc ... tcgtgagcagGAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCA
EST: gi|67571426|gb|BJ944250.1|BJ944250
EST:     TCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAG                         GAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCA
genomic: TCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAGgtattgctcc ... tcgtgagcagGAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCA
EST: gi|100409561|gb|BY955993.1|BY955993
EST:     TCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAG                         GAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCA
genomic: TCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAGgtattgctcc ... tcgtgagcagGAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCA

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: 34 (upstream exon), 32 (downstream exon)
Score: 18

CAGGCACGCAAAGGAGTGCTGTGAATTGAGGGTAGTGAGCAGTTGTGTGTTCGTTTTTGGCGACAAGGTGGATCAATCAAGTCACGAAAGATGGGAAGAGgtattgctcc ... tcgtgagcagGAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCAACGGCTTCGGCCGCTTCGGTCGTTTGGTTGCTAGAGTCGCTCTAGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtaatagtgatcgttgattgaaaactgagtcttgtgccttcttcgtgagcagGAACAAAGACTCCACCAGCCTCTCCAAAGGAGAAGCTTCGAATCGGTATCAACGGCTTCGGCCGCTTCGGTCGTTTGGTTGCTAGAGTCGCTCTAGAGAG
              cgttgat  putative branch site (score: 18)
 tcttgtgccttcttc  putative PPT
 attgaaaa  TA-rich tract