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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAGgtacgatctgtcattgagttgaattgtgaatgtggagccttccttttgcacatatagtggttgcgtgggccatttttacgttttttcgaggcaccatttgaggcttaagtcatgtaggaagcaaaatgattaatgttcatgttatgggtttgcggttgcag

Basic information

species Physcomitrella patens
transcript PP1S218_59V6.1
intron # 8
splice site 5'
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|162198108|gb|FC372135.1|FC372135
EST:     TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG                         AGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
genomic: TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAGgtacgatctg ... gcggttgcagAGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
EST: gi|100448067|gb|CJ972366.1|CJ972366
EST:     TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG                         AGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
genomic: TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAGgtacgatctg ... gcggttgcagAGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
EST: gi|100374074|gb|BY967923.1|BY967923
EST:     TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG                         AGAATCAACATTCAGGANATTAAAAACCATGAATGGTTTTTGAAGA-TTTA
genomic: TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAGgtacgatctg ... gcggttgcagAGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
EST: gi|162273708|gb|FC449431.1|FC449431
EST:     TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG                         AGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
genomic: TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAGgtacgatctg ... gcggttgcagAGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
EST: gi|162268987|gb|FC445479.1|FC445479
EST:     TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG                         AGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
genomic: TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAGgtacgatctg ... gcggttgcagAGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
EST: gi|162258201|gb|FC434232.1|FC434232
EST:     GGAATGCANGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCNTA-G                         AGAATCAACATTC
genomic: GGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGC-TAAGgtacgatctg ... gcggttgcagAGAATCAACATTC
EST: gi|162264918|gb|FC440693.1|FC440693
EST:     TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG                         AGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA
genomic: TGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAGgtacgatctg ... gcggttgcagAGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTA

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), 34 (downstream exon)
Score: 93

CGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAGgtacgatctg ... gcggttgcagAGAATCAACATTCAGGAAATTAAAAACCATGAATGGTTTTTGAAGAATTTACCAGCAGATCTCGTGGATCTTGCCGACAGGAGTTACGACTTTGAGGATC




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