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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaactgttgatttgaatgcgatcccataggcatttatgtatttctacgcagaggatgtttggtttggttttatgtcaatgagtgtttgttaggaatgttgggagtgacatattgagcatcgtgtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTCAATTGATTGGTGGTAGGCCGGGGCGAGACGTAGTGTAGTTCCGTGCTGG

Basic information

species Physcomitrella patens
transcript PP1S201_25V6.1
intron # 5
splice site 3'
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|208397825|gb|DC916160.1|DC916160
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|162232156|gb|FC408031.1|FC408031
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|208379881|gb|DC927607.1|DC927607
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|208396625|gb|DC924293.1|DC924293
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTNTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|162252871|gb|FC429244.1|FC429244
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|67694367|gb|BJ954600.1|BJ954600
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|208365604|gb|DC944102.1|DC944102
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|208348120|gb|DC916930.1|DC916930
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|162228075|gb|FC404643.1|FC404643
EST:     TAGGCGACGCCCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTTTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
EST: gi|67694695|gb|BJ954928.1|BJ954928
EST:     TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAG                         TGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC
genomic: TAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTC

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), 35 (downstream exon)
Score: 42

ACTACTTAGAGATAATCTGACTTTATGGACGTCAGATCTCCAGGACGATGTAGGCGACGACCAGGGAAAGGGAGATGACATGAGACCGGAGGAAGCGGAGgtacgaactg ... gtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTCAATTGATTGGTGGTAGGCCGGGGCGAGACGTAGTGTAGTTCCGTGCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgagtgtttgttaggaatgttgggagtgacatattgagcatcgtgtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTCAATTGATTGGTGGTAGGCCGGGGCGAGACGTAGTGTAGTTCCGTGCTGG
       tttgtta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaactgttgatttgaatgcgatcccataggcatttatgtatttctacgcagaggatgtttggtttggttttatgtcaatgagtgtttgttaggaatgttgggagtgacatattgagcatcgtgtgaatgcagTGATCACGACAATCAAGTCTTTTCTGATGGGGTGGATTCGGAAAGAGCCTCAATTGATTGGTGGTAGGCCGGGGCGAGACGTAGTGTAGTTCCGTGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG