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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcgtcgtttgcagggcgggaaggtcggaggtccgcatcacagcatcaacataggccacgagctctgatacaaggatggtgcttatgttgtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATAAGACCTATTTCACGAGTGCATTCTCTGGGTACACAGTAGGCCTTCTAGT

Basic information

species Physcomitrella patens
transcript PP1S47_5V6.2
intron # 9
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|37836833|gb|BJ594841.1|BJ594841
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|208363383|gb|DC946981.1|DC946981
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|208385887|gb|DC956725.1|DC956725
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|208353491|gb|DC922503.1|DC922503
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|208364937|gb|DC947079.1|DC947079
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|67696009|gb|BJ956242.1|BJ956242
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|162248338|gb|FC422553.1|FC422553
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|37836672|gb|BJ594680.1|BJ594680
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|37826376|gb|BJ584388.1|BJ584388
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|162211219|gb|FC386931.1|FC386931
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
EST: gi|208358589|gb|DC946550.1|DC946550
EST:     TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAG                         GCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA
genomic: TGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATA

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), 32 (downstream exon)
Score: 11

CTGATTTTTCCAACTGGTGATGTTACCCGGCCTTTCTCTATGCTGGGACTAGGGGACATTGTAATTCCAGgtgctcactc ... gtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATAAGACCTATTTCACGAGTGCATTCTCTGGGTACACAGTAGGCCTTCTAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaacataggccacgagctctgatacaaggatggtgcttatgttgtgagcgcagGCATTTTTGTAGCTTTGGCGTTGCGCTTTGATATGTCGAGGGGTCGGGATAAGACCTATTTCACGAGTGCATTCTCTGGGTACACAGTAGGCCTTCTAGT
                  ctctgat  putative branch site (score: 11)
                                      ttatgtt  TA-rich tract