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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgagcagaattaacattaaatttcactgtggccatatactgttcgacattgcatttgagcatctgttttcatgcaatttgatcaaagctattgcttccagATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAAATATTTGAAAGCACTTCCTCGGATCAAACTGGGATGCGCAATCGTTAAA

Basic information

species Physcomitrella patens
transcript PP1S79_21V6.1
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|208362999|gb|DC946896.1|DC946896
EST:     TTGCCGAGCGCCTTGTCCTTCCCATTCACAGCGACCTGGATGCAGATCAG                         ATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAA
genomic: TTGCCGAGCGCCTTGTCCTTCCCATTCACAGCGACCTGGATGCAGATCAGgtgtgtaatc ... ttgcttccagATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAA
EST: gi|18336374|gb|BJ168396.1|BJ168396
EST:     TTGCCGAGCGCCTTGTCCTTCCCATTCACAGCGACCTGGATGCAGATCAG                         ATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAA
genomic: TTGCCGAGCGCCTTGTCCTTCCCATTCACAGCGACCTGGATGCAGATCAGgtgtgtaatc ... ttgcttccagATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAA
EST: gi|208369857|gb|DC944237.1|DC944237
EST:     TTGCCGAGCGCCTTGTCCTTCCCATTCACAGCGACCTGGATGCAGATCAG                         ATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAA
genomic: TTGCCGAGCGCCTTGTCCTTCCCATTCACAGCGACCTGGATGCAGATCAGgtgtgtaatc ... ttgcttccagATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAA

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: 22 (upstream exon), 14 (downstream exon)
Score: 1

TACATTTGCTGGCGGTGAAGTGGAACAAGTTCCTGCATCATACATTGAATTTGCCGAGCGCCTTGTCCTTCCCATTCACAGCGACCTGGATGCAGATCAGgtgtgtaatc ... ttgcttccagATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAAATATTTGAAAGCACTTCCTCGGATCAAACTGGGATGCGCAATCGTTAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgcatttgagcatctgttttcatgcaatttgatcaaagctattgcttccagATCCACGAATGGCATCGTCGAGATGGTTTCGAAGTGGGCAACGCTGATAAAATATTTGAAAGCACTTCCTCGGATCAAACTGGGATGCGCAATCGTTAAA
                              atttgat  putative branch site (score: 1)
                                             ttgcttcc  putative PPT
                             aatttgat  TA-rich tract