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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACTGGTGCCGTATTATTTGGCTGAGGAGGATAACTGGGGTTTGAATACTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggctcactcatacttttacaaaccttgtttccgttgtggtctctggcggggcctatcgtggaacaaggaattatcggatgttagaaatgtcct...

Basic information

species Physcomitrella patens
transcript PP1S215_28V6.1
intron # 6
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|100393479|gb|BY953418.1|BY953418
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGT                         GTCCGAAGATTGGTTTTTATTCA-TCCAG-AAATCCAACTGGTCAATGTCT
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTAT-CAATCCAGGAAATCCAACTGGTCAATGTCT
EST: gi|162214587|gb|FC390618.1|FC390618
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAAGATTGGTTTTTATCAATCCA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCA
EST: gi|100417952|gb|BY993265.1|BY993265
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCANGAAGGGGATTTGT                         GTCCGAAGATTGGTTTTTATNCA-TCCAGGAAATCCAACTGGTCAATGTCT
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTAT-CAATCCAGGAAATCCAACTGGTCAATGTCT
EST: gi|162151638|gb|FC327767.1|FC327767
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATNCA-TCCAGGAAATCCAACTGGTCAATGTCT
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTAT-CAATCCAGGAAATCCAACTGGTCAATGTCT
EST: gi|162153918|gb|FC329425.1|FC329425
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAAGATTGGTTT
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTT
EST: gi|100392222|gb|BY953255.1|BY953255
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGT                         GTCCGAGGATTGGTTTT-ATCAATCCAGGAAATCCA-CTGGGTCA-TGTCT
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGG-TCAATGTCT
EST: gi|162152068|gb|FC328463.1|FC328463
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGANATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162155922|gb|FC332471.1|FC332471
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162176654|gb|FC352499.1|FC352499
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162178885|gb|FC354817.1|FC354817
EST:     GTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
genomic: GTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162186162|gb|FC361366.1|FC361366
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162177756|gb|FC354590.1|FC354590
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTTATCA-TCCA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTT-ATCAATCCA
EST: gi|162178101|gb|FC354403.1|FC354403
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162161643|gb|FC339058.1|FC339058
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGANATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162269857|gb|FC445387.1|FC445387
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGT                         GTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162217937|gb|FC393933.1|FC393933
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
EST: gi|162151906|gb|FC328152.1|FC328152
EST:     CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGC                         GTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA
genomic: CTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTA

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), 35 (downstream exon)
Score: 29

CACACTGGTGCCGTATTATTTGGCTGAGGAGGATAACTGGGGTTTGAATACTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggc ... gttgttttagGTCCGAGGATTGGTTTTTATCAATCCAGGAAATCCAACTGGTCAATGTCTAACCGAGAAAAATTTGCGGGAACTTATCGAGTTCTGCATCAAGGAAAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACTGGTGCCGTATTATTTGGCTGAGGAGGATAACTGGGGTTTGAATACTAATGACCTGCGTAAATCTGTCACTGAAGCTCGCAGGAAGGGGATTTGTgtaagttggctcactcatacttttacaaaccttgtttccgttgtggtctctggcggggcctatcgtggaacaaggaattatcggatgttagaaatgtcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC