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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTATGCATTGAGCTTTTACATCCCATGGGACAGGACGGCCCAGTTGCTGAATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttctacccatcctgtggaacacatttgtaatttgttctcaacaatttgcaagtctaacttatcaccaatctgtatttcag

Basic information

species Physcomitrella patens
transcript PP1S9_16V6.4
intron # 3
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|162245346|gb|FC423016.1|FC423016
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162254334|gb|FC430469.1|FC430469
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|67719288|gb|BJ969547.1|BJ969547
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162188463|gb|FC365061.1|FC365061
EST:     GAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: GAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162170966|gb|FC346657.1|FC346657
EST:     ATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: ATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|7067293|gb|AW497148.1|AW497148
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100451902|gb|CJ974999.1|CJ974999
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATA-TATCA-CTCAGCAGCATGCTACATAGGTG
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTG
EST: gi|161979081|gb|EE296290.1|EE296290
EST:     AATTTCTCGAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATANGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|18344184|gb|BJ176223.1|BJ176223
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGT
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGT
EST: gi|162161109|gb|FC336457.1|FC336457
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162183245|gb|FC360395.1|FC360395
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162206596|gb|FC382354.1|FC382354
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|208348623|gb|DC905860.1|DC905860
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162231984|gb|FC409058.1|FC409058
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100384389|gb|BY969520.1|BY969520
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GGCGATAATATCAACTCAGCAGCATTGCTAC
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCAT-GCTAC
EST: gi|208358492|gb|DC930624.1|DC930624
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100361217|gb|BY946972.1|BY946972
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162222955|gb|FC399612.1|FC399612
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162241531|gb|FC414679.1|FC414679
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100386386|gb|BY988053.1|BY988053
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACT
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACT
EST: gi|18325012|gb|BJ157008.1|BJ157008
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTAC
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTAC
EST: gi|162249732|gb|FC425611.1|FC425611
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100397059|gb|BY953964.1|BY953964
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100375769|gb|BY968182.1|BY968182
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCACGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100361088|gb|BY946908.1|BY946908
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100424206|gb|BY958368.1|BY958368
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGANTA-TATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGG
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGA-TAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGG
EST: gi|162210861|gb|FC387271.1|FC387271
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162222954|gb|FC399611.1|FC399611
EST:     ATTTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: A-TTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162184692|gb|FC361930.1|FC361930
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162245345|gb|FC423015.1|FC423015
EST:     CAAGAACATTCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: CAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|208353524|gb|DC938717.1|DC938717
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162167479|gb|FC344196.1|FC344196
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100385820|gb|BY951014.1|BY951014
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100365734|gb|BY948385.1|BY948385
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|162188462|gb|FC365060.1|FC365060
EST:     GCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: GCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100446199|gb|CJ970498.1|CJ970498
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100371594|gb|BY968056.1|BY968056
EST:     TTTCTCAAGAAACA-TCC-AACGGTGGCATCCATCACGTCTCATTTTGCG                         -TCGATTATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGG
genomic: TTTCTCAAGAA-CAATCCCAACGGTGGCATCCATCACGTCTCATTT-GCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGG
EST: gi|18374583|gb|BJ206161.1|BJ206161
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGA
EST: gi|100451910|gb|CJ975004.1|CJ975004
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATA-TATCA-CTCAGCAGCATGCTACATA
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATA
EST: gi|100427726|gb|BY977642.1|BY977642
EST:     AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCG                         GTCGATAATATTAACTCAGCAGCATGCTACATAGG
genomic: AATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGG

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), 33 (downstream exon)
Score: 70

TGTATGCATTGAGCTTTTACATCCCATGGGACAGGACGGCCCAGTTGCTGAATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttct ... tgtatttcagGTCGATAATATCAACTCAGCAGCATGCTACATAGGTGAAGCAGGCGTGGGAAGCATTCCTACTGGCAACCCTAATATAGGAGCAAGTTACAAATCTGAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTATGCATTGAGCTTTTACATCCCATGGGACAGGACGGCCCAGTTGCTGAATTTCTCAAGAACAATCCCAACGGTGGCATCCATCACGTCTCATTTGCGgtatggttctacccatcctgtggaacacatttgtaatttgttctcaacaatttgcaagtctaacttatcaccaatctgtatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC