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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgctttcacaaagactgaccaagcgagatcctggctgccgaacattgttcaatatttggaggaaaactagagttctaatcgtgtatctcgtgtttgtagGTGACGACAATGTTTCATCTTGATCGTCCAATGTATCTACTTGGATATCTCGCAAGTCAAAGCCGCGTGTATCTTATCGATAAGCAGTTAAA

Basic information

species Physcomitrella patens
transcript PP1S243_63V6.1
intron # 15
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|162174017|gb|FC350532.1|FC350532
EST:     TCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAG                         GTGACGACAATGTTTCATCTTGATCGTCCAATGTATCTA
genomic: TCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAGgtaagtaatg ... gtgtttgtagGTGACGACAATGTTTCATCTTGATCGTCCAATGTATCTA
EST: gi|162157189|gb|FC332823.1|FC332823
EST:     TCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAG                         GTGACGACAATGTTTCATCTTGATCGTCCAATGTATCTACTTGGATATCTC
genomic: TCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAGgtaagtaatg ... gtgtttgtagGTGACGACAATGTTTCATCTTGATCGTCCAATGTATCTACTTGGATATCTC
EST: gi|100430581|gb|BY978291.1|BY978291
EST:     TCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAG                         GTGACGACNATGTTTCATCTTGATCGTCCAATGTATCTA
genomic: TCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAGgtaagtaatg ... gtgtttgtagGTGACGACAATGTTTCATCTTGATCGTCCAATGTATCTA

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: 32 (upstream exon), 24 (downstream exon)
Score: 4

GCACGAAATTCCTGAGCGAATTAGAACTGGCTTGTGGGTTGGTGACTGCTTCATTTACAACAATTCAGCATGGAGACTCAACTACTGTGTTGGTGGAGAGgtaagtaatg ... gtgtttgtagGTGACGACAATGTTTCATCTTGATCGTCCAATGTATCTACTTGGATATCTCGCAAGTCAAAGCCGCGTGTATCTTATCGATAAGCAGTTAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcaatatttggaggaaaactagagttctaatcgtgtatctcgtgtttgtagGTGACGACAATGTTTCATCTTGATCGTCCAATGTATCTACTTGGATATCTCGCAAGTCAAAGCCGCGTGTATCTTATCGATAAGCAGTTAAA
                            ttctaat  putative branch site (score: 4)
      aatattt  TA-rich tract