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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttgataaggctctgaatacgatgaacatgttccttaatgttgagagaatccatccctgtttgattacgacgaactaacgttttgtgatccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATTTCTGATCGAGGATACCGCTTCTCATTAGCAGGCTCTGCTGTTGCGTGTG

Basic information

species Physcomitrella patens
transcript PP1S42_16V6.1
intron # 3
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|100395346|gb|BY953691.1|BY953691
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|162231292|gb|FC406533.1|FC406533
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|100426955|gb|BY977448.1|BY977448
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|162237827|gb|FC412480.1|FC412480
EST:     AGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: AGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|18328243|gb|BJ160247.1|BJ160247
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCT
EST: gi|208363997|gb|DC939590.1|DC939590
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|208376982|gb|DC911050.1|DC911050
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|100423213|gb|BY958195.1|BY958195
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTC-ATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|100365178|gb|BY966849.1|BY966849
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GGTGCGGTAATGGCTATTCTGGCTATNGTT-CCATTTTTCAC-GCGAGGTA
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTAT-GTTTCCATTTT-CACCGCGAGGTA
EST: gi|100411477|gb|BY974655.1|BY974655
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|100406431|gb|BY955623.1|BY955623
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTTCAC-GCGAGGTAT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTT-CACCGCGAGGTAT
EST: gi|100444442|gb|BY964140.1|BY964140
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATNGTT-CCATTTTCACCGCGAGGTAT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTAT-GTTTCCATTTTCACCGCGAGGTAT
EST: gi|7207567|gb|AW561615.1|AW561615
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|100448633|gb|CJ972932.1|CJ972932
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|18367244|gb|BJ199325.1|BJ199325
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATCGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTAT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAAT-GGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTAT
EST: gi|100387757|gb|BY951757.1|BY951757
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
EST: gi|100403625|gb|BY955020.1|BY955020
EST:     GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGG                         GTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT
genomic: GCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATT

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: 8 (upstream exon), 33 (downstream exon)
Score: 2

TGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCACCTAGAGCTGATGGCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCTCAACAATGCATGGgtacgtttta ... tccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATTTCTGATCGAGGATACCGCTTCTCATTAGCAGGCTCTGCTGTTGCGTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagaatccatccctgtttgattacgacgaactaacgttttgtgatccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATTTCTGATCGAGGATACCGCTTCTCATTAGCAGGCTCTGCTGTTGCGTGTG
                             aactaac  putative branch site (score: 2)
                tttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttgataaggctctgaatacgatgaacatgttccttaatgttgagagaatccatccctgtttgattacgacgaactaacgttttgtgatccactgcagGTTGCGGTAATGGCTATTCTGGCTATGTTTCCATTTTCACCGCGAGGTATTTCTGATCGAGGATACCGCTTCTCATTAGCAGGCTCTGCTGTTGCGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT