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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatactgttttttttttttttttttttttttttttttatctacgtatgatcgaagtcagctgaaatctgaaacttttgcattttgattggattgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGATTCCTGTTGGGACAGATTCTCAG

Basic information

species Physcomitrella patens
transcript PP1S55_159V6.3
intron # 7
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|208365688|gb|DC944144.1|DC944144
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|162171977|gb|FC349257.1|FC349257
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37848016|gb|BJ606024.1|BJ606024
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37841565|gb|BJ599573.1|BJ599573
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|162179521|gb|FC356561.1|FC356561
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|162158828|gb|FC335351.1|FC335351
EST:     GGAAGAGTGTGGACCTTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|162174063|gb|FC350578.1|FC350578
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37846075|gb|BJ604083.1|BJ604083
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|162266763|gb|FC442279.1|FC442279
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37852089|gb|BJ610097.1|BJ610097
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37842080|gb|BJ600088.1|BJ600088
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|162179520|gb|FC356560.1|FC356560
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37846074|gb|BJ604082.1|BJ604082
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|162197969|gb|FC373984.1|FC373984
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37841159|gb|BJ599167.1|BJ599167
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|162162076|gb|FC338867.1|FC338867
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37852017|gb|BJ610025.1|BJ610025
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|37853578|gb|BJ611586.1|BJ611586
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
EST: gi|18341709|gb|BJ173744.1|BJ173744
EST:     GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGG                         ATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA
genomic: GGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGA

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: 31 (upstream exon), 30 (downstream exon)
Score: 7

TCGCTGATGGAAAACTTGGCTGGGAAGAGTGTGGACCCTACGATGCCATTCATGTCGGAGCTGCCGCAGCGGgtactgctta ... attgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGATTCCTGTTGGGACAGATTCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatcgaagtcagctgaaatctgaaacttttgcattttgattggattgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGATTCCTGTTGGGACAGATTCTCAG
                                   ttttgat  putative branch site (score: 7)
                                  attttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatactgttttttttttttttttttttttttttttttatctacgtatgatcgaagtcagctgaaatctgaaacttttgcattttgattggattgtgacagATCTCCCGGAAGCTCTGGTGCAGCAGCTGAAGCCAGGCGGTCGCATGGTGATTCCTGTTGGGACAGATTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC