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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATTGGTACTACCCGAGGGCCCGCACAACCATTCACCATCCAACAATCTCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAGgtatccttctgttgcctatcttatccttgtcgcacttgtggtgaatgctacgacgttgtggttcattgtagcgtggggtgatcattgaatgatgaaagag...

Basic information

species Physcomitrella patens
transcript PP1S78_7V6.1
intron # 1
splice site 5'
intron type U12 (go to U12 genes for details)

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|67709923|gb|BJ965739.1|BJ965739
EST:     TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAG                         TATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
genomic: TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAGgtatccttct ... tgcaacgcagTATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
EST: gi|100402366|gb|BY954800.1|BY954800
EST:     TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAG                         TATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
genomic: TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAGgtatccttct ... tgcaacgcagTATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
EST: gi|67569196|gb|BJ942020.1|BJ942020
EST:     TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAG                         TATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
genomic: TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAGgtatccttct ... tgcaacgcagTATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
EST: gi|100368907|gb|BY984937.1|BY984937
EST:     TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAG                         TATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
genomic: TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAGgtatccttct ... tgcaacgcagTATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
EST: gi|208376670|gb|DC932134.1|DC932134
EST:     TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAG                         TATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC
genomic: TCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAGgtatccttct ... tgcaacgcagTATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACC

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: 28 (upstream exon), 16 (downstream exon)
Score: 3

GAGATTGGTACTACCCGAGGGCCCGCACAACCATTCACCATCCAACAATCTCAGTTTGCGAGGCTCAGCAGTTCAAGGACAACCCGCTTTGCTCCTACAGgtatccttct ... tgcaacgcagTATGCGAGTACTCGAAGACTGAATTCACCCGGAAATGTTATATTCGTGACCACTTCAAACTCGTCCAGTCTCTTGTTTGTAGCGGCGTATCGCACTGTAC




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