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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattttttattttttattttttctcaattgtctcattccatagactgctaaaggccattgaattcccaccttgaattggagatgtgcctgtttattaatgttgataagtttcgaaagattgtagagcgctgactgaacactctttcctaaatgttctccttatggttctcttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAACTTGTTTTCAGACTGGGAATCTGCGTTAGCTACTGAGGCCAAGATGAAAG

Basic information

species Physcomitrella patens
transcript PP1S61_1V6.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
gtatgtattttttattttttattttttctcaattgtctcattccatagactgctaaaggccattgaattcccaccttgaattggagatgtgcctgtttattaatgttgataagtttcgaaagattgtagagcgctgactgaacactctttcctaaatgttctccttatggt-tctcttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAACTTGTTTTCAGACTGGGAATCTGCGTTAGCTACTGAGGCCAAGATGAAAG
                                                                                |   | |||  ||     |  ||    ||||||     || ||  | || |       |||||   | ||| | | ||        ||| | ||    || |||| | | | |||| ||||||||||| ||||||||||| ||||| ||||| || ||||||   |||||| |   |||  | |  | |||  | || ||   ||
----------------------------------------------------------------------------catgtcataaatgaacc-----aagaaaagagataaggag-aaaggaaaggagtgaaaattttgaac---ccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG
















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|37827500|gb|BJ585512.1|BJ585512
EST:     NTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAG                         ATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATCCCCCAAC
genomic: CTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAGgtatgtattt ... cttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
EST: gi|162254475|gb|FC430675.1|FC430675
EST:     GCGCAATGATTTGAAGAAG                         ATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
genomic: GCGCAATGATTTGAAGAAGgtatgtattt ... cttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
EST: gi|162234002|gb|FC410710.1|FC410710
EST:     CTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAG                         ATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
genomic: CTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAGgtatgtattt ... cttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
EST: gi|67698796|gb|BJ959029.1|BJ959029
EST:     CTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAG                         ATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
genomic: CTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAGgtatgtattt ... cttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
EST: gi|162176146|gb|FC351901.1|FC351901
EST:     CTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAG                         ATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
genomic: CTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAGgtatgtattt ... cttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
EST: gi|162234001|gb|FC410709.1|FC410709
EST:     CGCAATGATTTGAAGAAG                         ATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC
genomic: CGCAATGATTTGAAGAAGgtatgtattt ... cttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAAC

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: 27 (upstream exon), 25 (downstream exon)
Score: 4

CAACCGTATCCCTGAAGCTGCATTTATGGCACGCACATATGCCCCTAGTCACGTGTCGAGAATAGTTTCTCTTTGGCGCAATGATTTGAAGAAGgtatgtattt ... cttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAACTTGTTTTCAGACTGGGAATCTGCGTTAGCTACTGAGGCCAAGATGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgctgactgaacactctttcctaaatgttctccttatggttctcttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAACTTGTTTTCAGACTGGGAATCTGCGTTAGCTACTGAGGCCAAGATGAAAG
                    tcctaaa  putative branch site (score: 4)
                             ttctccttatggttct  putative PPT
                       taaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtattttttattttttattttttctcaattgtctcattccatagactgctaaaggccattgaattcccaccttgaattggagatgtgcctgtttattaatgttgataagtttcgaaagattgtagagcgctgactgaacactctttcctaaatgttctccttatggttctcttttggcagATCAACCAAAAGGCTGCAGAATCTTTGGCAGATCCAGAAGAATACCCCAACTTGTTTTCAGACTGGGAATCTGCGTTAGCTACTGAGGCCAAGATGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG