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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctccctctctcattttcgtctggttatcttcagctatgttcagggtttggggtttaggaaacgcttgaattttacccgattctgatgaatgagttttgtttctgtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG

Basic information

species Physcomitrella patens
transcript PP1S13_236V6.1
intron # 1
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|37850086|gb|BJ608094.1|BJ608094
EST:     TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
EST: gi|37825316|gb|BJ583382.1|BJ583382
EST:     GGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: GGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
EST: gi|37852779|gb|BJ610787.1|BJ610787
EST:     GGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: GGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
EST: gi|162218184|gb|FC394189.1|FC394189
EST:     GGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: GGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
EST: gi|162169907|gb|FC345847.1|FC345847
EST:     TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
EST: gi|208387629|gb|DC953371.1|DC953371
EST:     TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
EST: gi|67692745|gb|BJ952978.1|BJ952978
EST:     TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
EST: gi|162218185|gb|FC394190.1|FC394190
EST:     TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
EST: gi|208370058|gb|DC940365.1|DC940365
EST:     TTCGTACTANAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTC                         ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
genomic: TTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG

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), 33 (downstream exon)
Score: 63

AGGCCTTCGCGGCAACCTCACCGTCACCATGGCGGAGAAAGCGTGCACCGTTCGTACTAGAAAGTTCATGACCAATCGCCTTCTGGCTCGCAAGCAATTCgtaagtgctc ... gtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacgcttgaattttacccgattctgatgaatgagttttgtttctgtttgggcagATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG
                     ttctgat  putative branch site (score: 63)
                                   ttttgtttctgttt  putative PPT
      ttgaatttta  TA-rich tract