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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggagcgcaagtttcccagcgttgcagttgtgttttttgaggatattttgttgctggggtagcttttgtgtcgctgacgctgctctgtggtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCGTGATGCCCGTCACGGCGTTCAAGATGGCGATCCCGAGGTCGTTTGTGTT

Basic information

species Physcomitrella patens
transcript PP1S4_93V6.2
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|18342503|gb|BJ174538.1|BJ174538
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|100422564|gb|BY976436.1|BY976436
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|100415259|gb|BY975228.1|BY975228
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|18354801|gb|BJ186859.1|BJ186859
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|18370193|gb|BJ201795.1|BJ201795
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|18351200|gb|BJ183251.1|BJ183251
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|100362010|gb|BY947738.1|BY947738
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|208361443|gb|DC930412.1|DC930412
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|100365166|gb|BY966843.1|BY966843
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|100353839|gb|BY983336.1|BY983336
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCACATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|18345110|gb|BJ177151.1|BJ177151
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|67718278|gb|BJ968537.1|BJ968537
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|162161556|gb|FC338763.1|FC338763
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
EST: gi|100440531|gb|BY962245.1|BY962245
EST:     AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAG                         TGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG
genomic: AATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCG

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: 34 (upstream exon), 35 (downstream exon)
Score: 25

CTTTTGCAACAAGCGCGGCAGTTTCCTCGTCTTGTGCGGGGCGCTGCTTGAATGCCACCGCAGCAACGCAGCCGAGGTGGAAGCCTGCTGGTTCATTAAGgtatgtttgc ... gtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCGTGATGCCCGTCACGGCGTTCAAGATGGCGATCCCGAGGTCGTTTGTGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgttgctggggtagcttttgtgtcgctgacgctgctctgtggtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCGTGATGCCCGTCACGGCGTTCAAGATGGCGATCCCGAGGTCGTTTGTGTT
                           cgctgac  putative branch site (score: 25)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggagcgcaagtttcccagcgttgcagttgtgttttttgaggatattttgttgctggggtagcttttgtgtcgctgacgctgctctgtggtcggtgcagTGGGTTGGGTCTAGGGATAACGCAGAGACTCTAAGTTTTTGGAGCTCATCGTGATGCCCGTCACGGCGTTCAAGATGGCGATCCCGAGGTCGTTTGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG