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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCCGATTGACGGTGGTGGGCTAATCGACGCATGATCCATGGCGACCACAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatctctatcctggaatcggtcagatcgataagattagagctctggtgcataatatgtgaatttgcaagcgtttagattctcaggtggaagttaa...

Basic information

species Physcomitrella patens
transcript PP1S41_70V6.1
intron # 1
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|18326829|gb|BJ158829.1|BJ158829
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|208353940|gb|DC930094.1|DC930094
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|162244584|gb|FC423446.1|FC423446
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|162184696|gb|FC361934.1|FC361934
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|67702629|gb|BJ962862.1|BJ962862
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|18351691|gb|BJ183743.1|BJ183743
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|67701947|gb|BJ962180.1|BJ962180
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGNTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGCGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|18327559|gb|BJ159562.1|BJ159562
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|67709266|gb|BJ965082.1|BJ965082
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|162244583|gb|FC423445.1|FC423445
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|162241395|gb|FC418560.1|FC418560
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA
EST: gi|18354254|gb|BJ186310.1|BJ186310
EST:     CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAG                         GNTGATTTGGCGGACTGCATCGAGTGGCAGNCTGTGGAATGTCTGAACGAA
genomic: CAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAA

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), 34 (downstream exon)
Score: 13

GTCTCCGATTGACGGTGGTGGGCTAATCGACGCATGATCCATGGCGACCACAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatct ... atttttgcagGTTGATTTGGCGGACTGCATCGAGTGGCAGTCTGTGGAATGTCTGAACGAAAATTCGTTGCATACCTCCGTCAACGCTCTTAAGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTCCGATTGACGGTGGTGGGCTAATCGACGCATGATCCATGGCGACCACAGCGACCCCCGCAACTACCGCCGCTCCAGTGCAGCTACCGTTAGGCCAGgtatgtatctctatcctggaatcggtcagatcgataagattagagctctggtgcataatatgtgaatttgcaagcgtttagattctcaggtggaagttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT