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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggacgaacaagttgtagggtttggtgtgtaggtgggttttgcgtgtttcgggttttgaattttcatctcatcgttgtttctgttcttgtggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATTCTACGTGACCATGGCGAAGAACTCTTTCAAGCAAGAGCATCCGCTGG

Basic information

species Physcomitrella patens
transcript PP1S26_103V6.1
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|18344066|gb|BJ176105.1|BJ176105
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|67571088|gb|BJ943912.1|BJ943912
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|67571800|gb|BJ944624.1|BJ944624
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|162232018|gb|FC409092.1|FC409092
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|18352101|gb|BJ184155.1|BJ184155
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|18327459|gb|BJ159462.1|BJ159462
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|100376476|gb|BY986185.1|BY986185
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|18342266|gb|BJ174301.1|BJ174301
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCAAT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|162276592|gb|FC451975.1|FC451975
EST:     TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: TGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
EST: gi|162202124|gb|FC377525.1|FC377525
EST:     CGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCG                         GTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT
genomic: CGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATT

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: 31 (upstream exon), 35 (downstream exon)
Score: 64

CTACCCGATAGCCTTCATCGCATCGTATGCTTGACAGAGAGCACTGAAGTTGTAACGCCGTGTGCATATCGTGCGACTCGATTTCGTGGAATTTGCTGCGgtaggcggtt ... tggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATTCTACGTGACCATGGCGAAGAACTCTTTCAAGCAAGAGCATCCGCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcgggttttgaattttcatctcatcgttgtttctgttcttgtggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATTCTACGTGACCATGGCGAAGAACTCTTTCAAGCAAGAGCATCCGCTGG
                                       ttcttgt  CT-rich tract
         ttttgaattttcat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggacgaacaagttgtagggtttggtgtgtaggtgggttttgcgtgtttcgggttttgaattttcatctcatcgttgtttctgttcttgtggatgtcagGTGAAGGAGGATTGTCTCGTCGGAGGAAGTTTTAAGGTGTATCATCGCATTCTACGTGACCATGGCGAAGAACTCTTTCAAGCAAGAGCATCCGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA