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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAGCACTACCCCGGCCGAACAACCTTCTTTGTGATTATGGTCTGTATAGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtttcctggccagtttatttcaaattcttgcagtcgaaagatgccagtttctagctttgcactcctaagggcttggagcagctaagtacaagt...

Basic information

species Physcomitrella patens
transcript PP1S101_17V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_17V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA01G44930.1 (Glycine max), 5'ss of exon 1
ATCAAGCACTACCCCGGCCGAACAACCTTCTTTGTGATTATGGTCTGTATAGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtttcctggccagtttatttcaaattcttgcagtcgaaagatgccagtttctagctttgcactcctaagggcttggagcagctaagtacaagt-------
  |    | | |   | |  ||  ||   | | || || ||    |||||  |||| ||  ||||||||||||||||||| ||||| |||||  ||||||||||| | | |  |   |   |  | ||    |||| |  | |||   ||  |||    ||||| |||||  |   |      ||||  ||| |    ||       
GCCGGAGATTTCGAGGCCAAAATCACTCCCATCGTCATCATTTCATGTATCATGGCTGCCACCGGAGGTCTCATGTTCGGCTACGACGTCGGCGTTTCAGgtaat-catcttttcttcttctcctctct--ctctttctttggaacagtggaagt----agcttggcacttgtgttgtgaaaaagcaattaattttgggtcggttaa
















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|100447665|gb|CJ971964.1|CJ971964
EST:     AGTGGCGGCATCCGGANGTCTCATGTTCGGATACGATGTCGGAATTTCAG                         GGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCCTGCGGTGT
genomic: AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtt ... tctttcccagGGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCCTGCGGTGT
EST: gi|100363760|gb|BY966547.1|BY966547
EST:     AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAG                         GGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCCTGCGGTGT
genomic: AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtt ... tctttcccagGGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCCTGCGGTGT
EST: gi|208398902|gb|DC912061.1|DC912061
EST:     AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAG                         GGGGTGTCACGTCTATGGACGAATTT
genomic: AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtt ... tctttcccagGGGGTGTCACGTCTATGGACGAATTT
EST: gi|100384109|gb|BY950495.1|BY950495
EST:     AGTGGCGGCATCCGGAAGTCTCATGTTCGGATACGATGTCGGAATTTCAG                         GGGGTGTCACGTCTATTGACGAATTTTTGGCGAAATTTTTTCCTG
genomic: AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtt ... tctttcccagGGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCCTG
EST: gi|162256530|gb|FC432840.1|FC432840
EST:     AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAG                         GGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCCTGCGGTGT
genomic: AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtt ... tctttcccagGGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCCTGCGGTGT
EST: gi|100381382|gb|BY950100.1|BY950100
EST:     AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAANT-CAG                         GGGGTGTCACGTCTATGGACGAAATTTTGGCGAAATTTTTTCCCTGCG
genomic: AGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtt ... tctttcccagGGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCC-TGCG

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), 35 (downstream exon)
Score: 31

ATCAAGCACTACCCCGGCCGAACAACCTTCTTTGTGATTATGGTCTGTATAGTGGCGGCATCCGGAGGTCTCATGTTCGGATACGATGTCGGAATTTCAGgtaattcgtt ... tctttcccagGGGGTGTCACGTCTATGGACGAATTTTTGGCGAAATTTTTTCCTGCGGTGTTGGCGAAGAAGCGAGCAGAGGCAGCTTCGGAGAGCGCCTACTGCAAGTA




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