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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGACGCATACCATATGACAGATCCCCGCGCCGACGGGTTGGGTGTTTCCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctctgttcactcaggagtaaggcattctcaatattgaatgcaacagcgtccgcttgctaagcttgatgaccttcttcgttgcacctttaaacag...

Basic information

species Physcomitrella patens
transcript PP1S201_89V6.1
intron # 4
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|162194223|gb|FC371048.1|FC371048
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162193225|gb|FC372013.1|FC372013
EST:     CAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|67692896|gb|BJ953129.1|BJ953129
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|208380712|gb|DC919428.1|DC919428
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162277902|gb|FC453825.1|FC453825
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162182566|gb|FC357541.1|FC357541
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162160823|gb|FC336722.1|FC336722
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162192157|gb|FC368306.1|FC368306
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|37825167|gb|BJ583233.1|BJ583233
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162220365|gb|FC395733.1|FC395733
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162185812|gb|FC362368.1|FC362368
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162216433|gb|FC393266.1|FC393266
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162194224|gb|FC371049.1|FC371049
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|208370717|gb|DC948254.1|DC948254
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|67720443|gb|BJ970702.1|BJ970702
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162252117|gb|FC428356.1|FC428356
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|208373189|gb|DC945143.1|DC945143
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGTATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162239762|gb|FC417161.1|FC417161
EST:     GGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: GGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162184291|gb|FC359700.1|FC359700
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|208362900|gb|DC957911.1|DC957911
EST:     CCACGNGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGNTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162192703|gb|FC370100.1|FC370100
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|37835911|gb|BJ593923.1|BJ593923
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|67724232|gb|BJ974491.1|BJ974491
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162185811|gb|FC362367.1|FC362367
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162221824|gb|FC398391.1|FC398391
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162270068|gb|FC446768.1|FC446768
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162192156|gb|FC368305.1|FC368305
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|208363288|gb|DC954418.1|DC954418
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162267460|gb|FC444211.1|FC444211
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162277397|gb|FC453203.1|FC453203
EST:     TGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: TGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162190912|gb|FC368110.1|FC368110
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162190722|gb|FC367608.1|FC367608
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162182298|gb|FC357169.1|FC357169
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162216432|gb|FC393265.1|FC393265
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162155215|gb|FC331698.1|FC331698
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162192702|gb|FC370099.1|FC370099
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
EST: gi|162190913|gb|FC368111.1|FC368111
EST:     CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAG                         GTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG
genomic: CCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCG

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), 30 (downstream exon)
Score: 14

GTGTGACGCATACCATATGACAGATCCCCGCGCCGACGGGTTGGGTGTTTCCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctct ... gaatttacagGTTAACTACATTAATGCGCATGCTACATCTACAGTCGTGGGTGATTTAGCGGAAGTGAACGCCATTAAGAAGGTCTTCAAAAACACATCAGAGATTAAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGACGCATACCATATGACAGATCCCCGCGCCGACGGGTTGGGTGTTTCCACGTGTATTGAGAAGAGTTTGGCAGATGCAGGAGTCGCCACTGAGGAGgtatttctctgttcactcaggagtaaggcattctcaatattgaatgcaacagcgtccgcttgctaagcttgatgaccttcttcgttgcacctttaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG