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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccgaacgtcgtgaacgcatggtcattatcaaagtcagtcgctttggtttcgtttccatcactgcgccgaggaaggctttgggtattgcagtgtgcaccgatgtggctgatttgtgacgtgttttgggactggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG

Basic information

species Physcomitrella patens
transcript PP1S167_1V6.1
intron # 6
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|162239319|gb|FC415405.1|FC415405
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATTTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|100411963|gb|BY992426.1|BY992426
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATCTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|208391457|gb|DC937605.1|DC937605
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAANAGAGTCANG                         TTGTACGCCGANTCNATGGCACGGTCCCAGGGG
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGG
EST: gi|100386544|gb|BY951340.1|BY951340
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAAAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCC
EST: gi|100420810|gb|BY993515.1|BY993515
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATTTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|162249711|gb|FC426825.1|FC426825
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATTTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|162167541|gb|FC343712.1|FC343712
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATTTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|67726787|gb|BJ977046.1|BJ977046
EST:     GGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATTTAC
genomic: GGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|162202240|gb|FC378096.1|FC378096
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAAAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATTTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|208400746|gb|DC904924.1|DC904924
EST:     TGATCGGTTCTTGTCGGANCCAGCGTTGGACTTTGTGAA-AGGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCAGG
genomic: TGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAG-AGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGG
EST: gi|162179697|gb|FC355755.1|FC355755
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATTTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|100410627|gb|BY992191.1|BY992191
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATCTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|208359628|gb|DC934615.1|DC934615
EST:     ATGATCGGTTCTTGTCGGANCCAGCGTTGGACTTTGTGAAAAAAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCNAGGGGGG-TCGCCGTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTAC
EST: gi|208370153|gb|DC951752.1|DC951752
EST:     GCCAGCGTT-GACTTTGTGAAGAGAGTCAAG                         -TGTACGCCGAGTCGATGGCACGGTTCCA-GGGGGGTCGCCGTACA-TTAC
genomic: GCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC
EST: gi|162194881|gb|FC368998.1|FC368998
EST:     ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAAAGAGTCAAG                         TTGTACGCCGAGTCGATGGCACGGTTCCANNNNNNNTCGCCGTACATTTAC
genomic: ATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTAC

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), 35 (downstream exon)
Score: 33

GGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGCTCTGCATCGCGATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTGAAGAGAGTCAAGgtatgccgaa ... actggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcagtgtgcaccgatgtggctgatttgtgacgtgttttgggactggtgcagTTGTACGCCGAGTCGATGGCACGGTTCCAGGGGGGGTCGCCGTACATTTACCCGCTGTATGGTCTCGGCGAGTTGCCGCAG
                     ggctgat  putative branch site (score: 33)