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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaggacaattgtgaccttgtggttcacgtagcgtgagaaccctgattcgctgtatgcagctgacataaatgggatgacgcatggatgatgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAGTTGCCTTCTTCTCCGATTTGCG

Basic information

species Physcomitrella patens
transcript PP1S91_243V6.1
intron # 1
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|208377196|gb|DC932346.1|DC932346
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|100365370|gb|BY966564.1|BY966564
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|208394189|gb|DC933857.1|DC933857
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|100427223|gb|BY959037.1|BY959037
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|162190479|gb|FC365701.1|FC365701
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|162150706|gb|FC327602.1|FC327602
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|100429270|gb|BY978026.1|BY978026
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|100375926|gb|BY968230.1|BY968230
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|18342722|gb|BJ174757.1|BJ174757
EST:     GCAGCANGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|208376325|gb|DC940995.1|DC940995
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|208366816|gb|DC940130.1|DC940130
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|100435552|gb|BY960970.1|BY960970
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|100405284|gb|BY955448.1|BY955448
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|67703540|gb|BJ963773.1|BJ963773
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|67508428|gb|BJ941295.1|BJ941295
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|100388728|gb|BY970876.1|BY970876
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|208359364|gb|DC939117.1|DC939117
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|208369746|gb|DC941008.1|DC941008
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|67569192|gb|BJ942016.1|BJ942016
EST:     GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: GCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
EST: gi|67571758|gb|BJ944582.1|BJ944582
EST:     CGATCCGGACGACACGATGAATCCCGAATA                         TGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG
genomic: CGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAG

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), 34 (downstream exon)
Score: 70

TCGCGGTGCGTTGCTCGTAGCGGCAGATCGGAGCGGGCTGAGGGCGGAAGGCAGCAGGTCGCGAGAGCGCCGATCCGGACGACACGATGAATCCCGAATAgtgagttgct ... tgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAGTTGCCTTCTTCTCCGATTTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcgctgtatgcagctgacataaatgggatgacgcatggatgatgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAGTTGCCTTCTTCTCCGATTTGCG
              agctgac  putative branch site (score: 70)
                   acataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaggacaattgtgaccttgtggttcacgtagcgtgagaaccctgattcgctgtatgcagctgacataaatgggatgacgcatggatgatgttttgcagTGACTACCTTTTTAAGCTTTTGCTGATTGGAGATTCTGGTGTGGGAAAGAGTTGCCTTCTTCTCCGATTTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT