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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacattcacttgtcgtatcaccagttctcattagttgtagttgttttcaccatgtattttatagaatcccatggagagtaagtgttccagcccattgatctctttcctcgatttgcagTTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGGTTCGTTCGTGGACAATTCGATCCGTCGTCTAAG

Basic information

species Physcomitrella patens
transcript PP1S97_119V6.1
intron # 2
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|100409984|gb|BY974351.1|BY974351
EST:     TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAG                         TTTAGT-CTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCG
genomic: TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAGgttacattca ... cgatttgcagTT-AGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCG
EST: gi|37827510|gb|BJ585522.1|BJ585522
EST:     TGCACACNTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAG                         TTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGG
genomic: TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAGgttacattca ... cgatttgcagTTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGG
EST: gi|208370967|gb|DC944342.1|DC944342
EST:     TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAG                         TTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGG
genomic: TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAGgttacattca ... cgatttgcagTTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGG
EST: gi|208351094|gb|DC921340.1|DC921340
EST:     TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAG                         TTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGG
genomic: TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAGgttacattca ... cgatttgcagTTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGG
EST: gi|208384842|gb|DC907455.1|DC907455
EST:     TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAG                         TTAGTTCTGTTGGGTGACTCAGGA
genomic: TGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAGgttacattca ... cgatttgcagTTAGTTCTGTTGGGTGACTCAGGA

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), 35 (downstream exon)
Score: 6

CTGCTGTGAAAGGCTCTGGGCGCTTGCACACCTCTCAGGCTGAAGCTTTGGATTCCAAACAAATACGAATCAAGgttacattca ... cgatttgcagTTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGGTTCGTTCGTGGACAATTCGATCCGTCGTCTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatcccatggagagtaagtgttccagcccattgatctctttcctcgatttgcagTTAGTTCTGTTGGGTGACTCAGGAGTCGGGAAGAGCTGCATTCTCTTGCGGTTCGTTCGTGGACAATTCGATCCGTCGTCTAAG
                             cattgat  putative branch site (score: 6)
                                   tctctttcctcgattt  CT-rich tract