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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagagaaacctggtcttagaccagctgggttgacgcatttacaaatatcgttttgatacattcttttactgagcctgcttgtttgtttgtgtccgcacagGTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCACG

Basic information

species Physcomitrella patens
transcript PP1S72_25V6.1
intron # 1
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|100397837|gb|BY990426.1|BY990426
EST:     GAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACG                         GTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA
genomic: GAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACGgtgagttgga ... gtccgcacagGTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA
EST: gi|100447682|gb|CJ971981.1|CJ971981
EST:     GAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACG                         GTTGTATGCTCCANTATGCCCTTCTTCACCTGGCANGATACGACAGTGTCA
genomic: GAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACGgtgagttgga ... gtccgcacagGTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA
EST: gi|67716179|gb|BJ966439.1|BJ966439
EST:     ACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACG                         GTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA
genomic: ACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACGgtgagttgga ... gtccgcacagGTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA
EST: gi|162255769|gb|FC431429.1|FC431429
EST:     GAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACG                         GTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA
genomic: GAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACGgtgagttgga ... gtccgcacagGTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA
EST: gi|100390522|gb|BY952930.1|BY952930
EST:     GAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACG                         GTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA
genomic: GAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACGgtgagttgga ... gtccgcacagGTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCA

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), 34 (downstream exon)
Score: 71

GCTCCCATGGGCCACATTTTGTACGACGAGGTGATGAAGTACAACCCGAAGAACCCATACTGGTTCAACAGGGATCGATTCGTTCTGTCCGCCGGTCACGgtgagttgga ... gtccgcacagGTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcgttttgatacattcttttactgagcctgcttgtttgtttgtgtccgcacagGTTGTATGCTCCAGTATGCCCTTCTTCACCTGGCAGGATACGACAGTGTCACG
     ttttgat  putative branch site (score: 71)
              attctttta  TA-rich tract