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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacaagcagctcggatgctctcgtgttggtttcacaaggaactcagcacgtcgttttctgttcgaccgaatggtattcgaatgcgcgtgttattgtcgcagtcgtatcaggattgaatgaggcggttgtggtgtttctaagctcgactttgtttggttatgttgcagTGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCGTGAAGTCTGTTCGCGACTGTCTCGATGAGTATGCTTCGCTTTACATTTT

Basic information

species Physcomitrella patens
transcript PP1S431_4V6.1
intron # 1
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|18354793|gb|BJ186851.1|BJ186851
EST:     TGCCGCAAACGCCCCTTGCATCATGCCGAAGTCGAAGAGAAATAAGCTCG                         TGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCG
genomic: TGCCGCAAACGCCCCTTGCATCATGCCGAAGTCGAAGAGAAATAAGCTCGgtgagaacaa ... tatgttgcagTGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCG
EST: gi|208355823|gb|DC930186.1|DC930186
EST:     TGCCGCAAACGCCCCTTGCATCATGCCGAAGTCGAAGAGAAATAAGCTCG                         TGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCG
genomic: TGCCGCAAACGCCCCTTGCATCATGCCGAAGTCGAAGAGAAATAAGCTCGgtgagaacaa ... tatgttgcagTGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCG
EST: gi|18349399|gb|BJ181448.1|BJ181448
EST:     TGCCGCAAACGCCCCTTGCATCATGCCGAAGTCGAAGAGAAATAAGCTCG                         TGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCG
genomic: TGCCGCAAACGCCCCTTGCATCATGCCGAAGTCGAAGAGAAATAAGCTCGgtgagaacaa ... tatgttgcagTGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCG

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: 24 (upstream exon), 25 (downstream exon)
Score: 2

TGTTACTCCTGGCGTCAGGCGTCTGCTCATTTTGCGACATCGTGATCATCTGCCGCAAACGCCCCTTGCATCATGCCGAAGTCGAAGAGAAATAAGCTCGgtgagaacaa ... tatgttgcagTGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCGTGAAGTCTGTTCGCGACTGTCTCGATGAGTATGCTTCGCTTTACATTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatgaggcggttgtggtgtttctaagctcgactttgtttggttatgttgcagTGACTCTGTCGAAGACGAAGAAGAAGGGCAAGGAGCAGAAGGAGTCGCTCGTGAAGTCTGTTCGCGACTGTCTCGATGAGTATGCTTCGCTTTACATTTT
                     tttctaa  TA-rich tract