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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcttctctccaaatagttgtttcctaagtaacatgattctgtcttgatgtcattctgatatgttaatcttctagacctgacattacttgtggatctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGACCAAATGTTGGACATTCGG

Basic information

species Physcomitrella patens
transcript PP1S39_120V6.1
intron # 11
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|162181521|gb|FC358135.1|FC358135
EST:     GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|100379082|gb|BY986565.1|BY986565
EST:     GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|37851029|gb|BJ609037.1|BJ609037
EST:     GGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|162166326|gb|FC342919.1|FC342919
EST:     GGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|162182040|gb|FC356911.1|FC356911
EST:     GAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|162181520|gb|FC358134.1|FC358134
EST:     GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|162153392|gb|FC329902.1|FC329902
EST:     GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|162196480|gb|FC374406.1|FC374406
EST:     GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|162196479|gb|FC374405.1|FC374405
EST:     GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
EST: gi|162166327|gb|FC342920.1|FC342920
EST:     GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAA                         ATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA
genomic: GCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGA

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), 32 (downstream exon)
Score: 6

GACGTGAAGGCGAGTGGTCTGCCGAGGAGCTAGAGGAAGCTGCAGAGGCTCTGGGCTATGGCGCCATTAAgtaaatcttc ... atctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGACCAAATGTTGGACATTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcattctgatatgttaatcttctagacctgacattacttgtggatctatgtagATATGCGGATTTGAAGAATAACAGGTTGACAAATTATACCTTCAATTTCGACCAAATGTTGGACATTCGG
                           acctgac  putative branch site (score: 6)
          atatgttaat  TA-rich tract