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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttggttgttttcagttcttgtgcgacttggctatgtcgaacccgattaccgtgtacttttactaaaatgcagaaaaatctggaacaatgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAATGTTCCTCGCCCTGTGATCTTTGCTGAGCCAGTGACATCATCGAACTCTT

Basic information

species Physcomitrella patens
transcript PP1S179_27V6.2
intron # 14
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|162164217|gb|FC342032.1|FC342032
EST:     TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAG                         ATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
genomic: TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAGgtttgtttcc ... tgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
EST: gi|18325669|gb|BJ157666.1|BJ157666
EST:     TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAG                         ATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
genomic: TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAGgtttgtttcc ... tgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
EST: gi|162220368|gb|FC395736.1|FC395736
EST:     TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAG                         ATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
genomic: TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAGgtttgtttcc ... tgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
EST: gi|162166374|gb|FC342356.1|FC342356
EST:     TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAG                         ATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
genomic: TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAGgtttgtttcc ... tgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
EST: gi|100375508|gb|BY948893.1|BY948893
EST:     TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAG                         ATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
genomic: TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAGgtttgtttcc ... tgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
EST: gi|162197657|gb|FC374491.1|FC374491
EST:     TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAG                         ATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
genomic: TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAGgtttgtttcc ... tgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAAT
EST: gi|162199450|gb|FC373765.1|FC373765
EST:     TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAG                         ATGGTCACACCTCCGAAGCCNNNNNNNGAAAAGCAGGAAGAAGTCTAAGAA
genomic: TGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAGgtttgtttcc ... tgctgtgcagATGGTCACACCTCCGAAGCCAAAAAA-GAAAAGCAGGAAGAAGTCTAAGAA

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: 31 (upstream exon), 35 (downstream exon)
Score: 16

CTACAGAGACCTGAAGCCAGAAAACATCTTGGTCACAGCTAGTGGACATGTGCAACTCACTGATTTTGACCTGTCTTTCGTATCCTCACCTCGAGTGGAGgtttgtttcc ... tgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAATGTTCCTCGCCCTGTGATCTTTGCTGAGCCAGTGACATCATCGAACTCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattaccgtgtacttttactaaaatgcagaaaaatctggaacaatgctgtgcagATGGTCACACCTCCGAAGCCAAAAAAGAAAAGCAGGAAGAAGTCTAAGAATGTTCCTCGCCCTGTGATCTTTGCTGAGCCAGTGACATCATCGAACTCTT
                 tactaaa  putative branch site (score: 16)
           tacttttactaaaat  TA-rich tract