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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatattttacctcatggacattgcctcatttctatgttggtttttgtgttttggctctatgtttgaaaaatgctaaattgctatggagatactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATTGCAGTTGATTTGAGTGATGAAAGTGCCTATGCGGTGAAGTGGGCAGTGG

Basic information

species Physcomitrella patens
transcript PP1S98_214V6.1
intron # 2
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|162252229|gb|FC425907.1|FC425907
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTG                       
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---Ggtggttgttc ... tactttgc
EST: gi|208387788|gb|DC941357.1|DC941357
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGgtggttgttc ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162216213|gb|FC392630.1|FC392630
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGgtggttgttc ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162180414|gb|FC355835.1|FC355835
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGgtggttgttc ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|22492564|gb|BU052487.1|BU052487
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGgtggttgttc ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162207218|gb|FC382540.1|FC382540
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGgtggttgttc ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162245832|gb|FC420473.1|FC420473
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGgtggttgttc ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162239278|gb|FC416521.1|FC416521
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTG                       
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---Ggtggttgttc ... tactttgc
EST: gi|100403797|gb|BY955106.1|BY955106
EST:     AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: AGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGgtggttgttc ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT

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), 24 (downstream exon)
Score: 18

GGAATCTGCGGGACTAGAAGTAATCAAACGGTGTTGCACTTGCGATTGAAAGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGgtggttgttc ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATTGCAGTTGATTTGAGTGATGAAAGTGCCTATGCGGTGAAGTGGGCAGTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttttggctctatgtttgaaaaatgctaaattgctatggagatactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATTGCAGTTGATTTGAGTGATGAAAGTGCCTATGCGGTGAAGTGGGCAGTGG
                          tgctaaa  putative branch site (score: 18)
             tatgtttgaaaaat  TA-rich tract