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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgcatgtgcttgcaaggcttagcctgcttttccttatttatttatttgtttattttttggtaaagtatttacattttctatgtttcgtgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG

Basic information

species Physcomitrella patens
transcript PP1S232_73V6.1
intron # 3
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|37837097|gb|BJ595105.1|BJ595105
EST:     ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATG                         GCTAATAGCGGACCAAATACAAATGGATGTCAG
genomic: ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATGgtaatcacag ... tgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG
EST: gi|208367447|gb|DC954935.1|DC954935
EST:     ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATG                         GCTAATAGCGGACCAAATACAAATGGATGTCAG
genomic: ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATGgtaatcacag ... tgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG
EST: gi|208392090|gb|DC941938.1|DC941938
EST:     ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATG                         GCTAATAGCGGACCAAATACAAATGGATGTCAG
genomic: ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATGgtaatcacag ... tgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG
EST: gi|162278032|gb|FC453851.1|FC453851
EST:     ACGATGAGAACTTTATCGTTAAGCACACCGGTCCAGGGCTGCTTTTTATG                         GTTAATAGCGGACCAAATACAAATGGATGTCAG
genomic: ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATGgtaatcacag ... tgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG
EST: gi|37823252|gb|BJ581318.1|BJ581318
EST:     ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATG                         GCTAATAGCGGACCAAATACAAATGGATGTCAG
genomic: ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATGgtaatcacag ... tgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG
EST: gi|208388913|gb|DC932941.1|DC932941
EST:     ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATG                         GCTAATAGCGGACCAAATACAAATGGATGTCAG
genomic: ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATGgtaatcacag ... tgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG
EST: gi|162278033|gb|FC453852.1|FC453852
EST:     ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATG                         GCTAATAGCGGACCAAATACAAATGGATGTCAG
genomic: ACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATGgtaatcacag ... tgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG

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: 4

CGTGAAGGGAGATGGAAGTGGCTGCACCAGTATCTATGGAAGTAAATTTGACGATGAGAACTTTATCGCTAAGCACACCGGTCCAGGGCTGCTTTCTATGgtaatcacag ... tgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtttattttttggtaaagtatttacattttctatgtttcgtgtcttgtagGCTAATAGCGGACCAAATACAAATGGATGTCAG
      tttattttttggtaaa  TA-rich tract