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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaatcccacgtttttgaaattccttgatatttaaacaaaaactgtcttggatttatgttgtattctttaaacggaccttgagctgtaacttacacgtgttgctgttgtctacagATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTGGCTGGTCGCATGAGTTTTCATGTTTAAGATTTTTGTTTCTTAGCATTCG

Basic information

species Physcomitrella patens
transcript PP1S162_133V6.1
intron # 6
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|162156071|gb|FC332238.1|FC332238
EST:     AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
genomic: AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAGgtaagtgaat ... ttgtctacagATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
EST: gi|162152857|gb|FC328951.1|FC328951
EST:     AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
genomic: AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAGgtaagtgaat ... ttgtctacagATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
EST: gi|162237673|gb|FC413288.1|FC413288
EST:     AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
genomic: AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAGgtaagtgaat ... ttgtctacagATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
EST: gi|37846008|gb|BJ604016.1|BJ604016
EST:     AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
genomic: AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAGgtaagtgaat ... ttgtctacagATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
EST: gi|162218006|gb|FC393690.1|FC393690
EST:     AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG
genomic: AGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAGgtaagtgaat ... ttgtctacagATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTG

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: 16 (upstream exon), 28 (downstream exon)
Score: 4

GAGGAGCGGAGATTGTCTTTGCAGAAGTACCAGGTTCATGACGAAACAATTCAGgtaagtgaat ... ttgtctacagATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTGGCTGGTCGCATGAGTTTTCATGTTTAAGATTTTTGTTTCTTAGCATTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattctttaaacggaccttgagctgtaacttacacgtgttgctgttgtctacagATGAGTTCTGTTGATGCTGCAATTGATAAGAGGATTTTAGAAGGCAGGCTGGCTGGTCGCATGAGTTTTCATGTTTAAGATTTTTGTTTCTTAGCATTCG
                           aacttac  putative branch site (score: 4)
      tttaaa  TA-rich tract