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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACTGGGTGCGGGATGTTGCATGGGCTCCTAACCTTGGGCTCCCCAGGTCCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttttccaccaccacggcattatgcataaatcttttttttatcttctttaagctagtacacgctagaaatttttcatgacatgagtgcggtgtt...

Basic information

species Physcomitrella patens
transcript PP1S100_118V6.1
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|15728186|gb|BI740662.1|BI740662
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|37826278|gb|BJ584290.1|BJ584290
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|18337406|gb|BJ169430.1|BJ169430
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|37847002|gb|BJ605010.1|BJ605010
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|67579349|gb|BJ951480.1|BJ951480
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|37826060|gb|BJ584072.1|BJ584072
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|37839516|gb|BJ597524.1|BJ597524
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|162214350|gb|FC390069.1|FC390069
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATTTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|162214351|gb|FC390070.1|FC390070
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|37841336|gb|BJ599344.1|BJ599344
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|162221836|gb|FC398403.1|FC398403
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
EST: gi|37845060|gb|BJ603068.1|BJ603068
EST:     CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAG                         GCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC
genomic: CCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACC

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: 16 (upstream exon), 27 (downstream exon)
Score: 7

TGACTGGGTGCGGGATGTTGCATGGGCTCCTAACCTTGGGCTCCCCAGGTCCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttt ... tgaatttcagGCCAAAGACGGGGACCAGTGGCAGCCATTGACCTTAAATGACTTCAAGACCCCAGTGTGGCGAGTAAGCTGGTCTCTAACTGGAAACATACTAGCTGTAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACTGGGTGCGGGATGTTGCATGGGCTCCTAACCTTGGGCTCCCCAGGTCCACCATCGCTAGCGCATCTCAAGATGGAACTGTTGTTATCTGGACTCAGgtattagttttccaccaccacggcattatgcataaatcttttttttatcttctttaagctagtacacgctagaaatttttcatgacatgagtgcggtgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA