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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGTATCCGACTTTGGGCCTAAAACGGCTCTGAAGATTGTGGACACCATTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgtttcctcacctttaccgtcgtagttcttcttagactgaaaattatattaaattctcaatcgctgtttctgtctataaggaagcaggcttttaa...

Basic information

species Physcomitrella patens
transcript PP1S98_142V6.1
intron # 2
splice site 5'
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|18358653|gb|BJ190712.1|BJ190712
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|208381435|gb|DC927871.1|DC927871
EST:     GCAGGCAGGTNGAAGTCTGGACCACAGATCAAG                         GAAGCTTNGAAAAAGAANATATTTAANTTGTNAACTGAAAGAGTGACCACC
genomic: GCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|100406046|gb|BY991512.1|BY991512
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|208354010|gb|DC914122.1|DC914122
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|100362534|gb|BY947402.1|BY947402
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|100383126|gb|BY987023.1|BY987023
EST:     TCGCGAGGACATCCTCTG-AGGTAGGTTGAAGTCTGGACCACAGATCAAC                         GATAGCTTTGAAAAAGAATATA
genomic: TCGCAAGGACATCCTC-GCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGA-AGCTTTGAAAAAGAATATA
EST: gi|100436742|gb|BY979503.1|BY979503
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|100424608|gb|BY976725.1|BY976725
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|18347068|gb|BJ179114.1|BJ179114
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACC
EST: gi|18362592|gb|BJ194663.1|BJ194663
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTT
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTT
EST: gi|100405617|gb|BY973767.1|BY973767
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAAGA-TATATTTAAATTGTTAACTGAAAGAGTGACCAC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAA-GAATATATTTAAATTGTTAACTGAAAGAGTGACCAC
EST: gi|67574460|gb|BJ947284.1|BJ947284
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|162166212|gb|FC342623.1|FC342623
EST:     CATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: CATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|100391599|gb|BY989465.1|BY989465
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|100441955|gb|BY981178.1|BY981178
EST:     TTCGGAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAACAATATATTTAAATTGTTAACTGA
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGA
EST: gi|208353643|gb|DC938752.1|DC938752
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
EST: gi|18361896|gb|BJ193963.1|BJ193963
EST:     TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAG                         GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC
genomic: TTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACC

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), 15 (downstream exon)
Score: 4

GCTTGTATCCGACTTTGGGCCTAAAACGGCTCTGAAGATTGTGGACACCATTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgttt ... tgctctgaagGAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGTATCCGACTTTGGGCCTAAAACGGCTCTGAAGATTGTGGACACCATTCGCAAGGACATCCTCGCAGGCAGGTTGAAGTCTGGACCACAGATCAAGgttgatgtttcctcacctttaccgtcgtagttcttcttagactgaaaattatattaaattctcaatcgctgtttctgtctataaggaagcaggcttttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA