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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgacttattcgagcatctgaaaccttgatgaggtctgcttccgaaaattccctcataaacttaacagtgcgtttatgtatatcgggaactttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT

Basic information

species Physcomitrella patens
transcript PP1S267_10V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 5
----gcgacttattcgagcatctgaaaccttgatgaggtc-tgcttccg----aaaattccc-----tcataaacttaacagtgcgtttatgtatatcgggaactttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT
    | |  ||  | | |  |   ||| ||| |||  ||     ||| |    ||| || |      |  ||    |        | |||| |||| | |   | |    | |||  | |||||    ||| || | || || |   | ||||| ||||| ||||||||||| ||||| |||||||||||||||||  | || || ||||| ||
gtgcgtggtttggt-gtgtttgcaaaagcttcatggtgttgcatttctgttccaaagtttcatggtgttgtatttctgttccaaggcttat-tatacctgttgcatgttcgtagGGCTGATTGATCTTGCTATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGT

upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 5
gcgacttattcgagcatctgaaaccttgatgaggtctgcttccgaaaattccctcataaacttaacagtgcgt-ttatg-----tatatcgggaactttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT
                         || |||  ||    ||   |  | ||  | || || | || | ||    | |||     | |    ||   |||| || |||  |||||||    ||  |   ||| ||   | | || || || ||||| |||||||| || ||||||||||||||||||||  | || || ||||| ||
-----------------------gtttcatgtagttgagttttaatcactcattgatcaa-tcaatattggaaatcatgactgattttcttgggggtttgttgtagGTCTAATTGATATGGCGATCAGGAACAATGTTTTGATCGGTGGAGATGATTTCAAGAGTGGTCAAACCAAGATGAAATCTGTCTTGGTTGATTTCCTAGT

upper sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 5
gcgacttattcgagcatctgaaaccttgatgaggtctgcttccgaaaattccctcataaacttaacagtgcgtttatgtatatcgggaactttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT
|  ||| | |  | |     | | || |||    |      ||   ||||  || |||    | ||| |  | |||| |                | ||||  | ||||| |  ||  || |||  || |   | || || ||||||||||||||||| || || ||||||||||| ||||| || || || ||||| ||
gtaactaaattaaact----atatctagatagtattaatgaccttcaattttct-atagtaatcacattttgcttatatt--------------atacagGGCTTATTGAATTAGCCATAAAGAGAAACTGCTTGATCGGTGGTGATGACTTCAAGAGTGGTCAGACCAAGATGAAGTCTGTCCTCGTCGATTTCCTTGT

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|162226051|gb|FC401329.1|FC401329
EST:     CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCG                         GCGTAATTGAGTACGCTGT
genomic: CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGT
EST: gi|162172373|gb|FC348314.1|FC348314
EST:     CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCG                         GCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
genomic: CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
EST: gi|162269000|gb|FC445492.1|FC445492
EST:     CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCG                         GCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
genomic: CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
EST: gi|162150742|gb|FC327014.1|FC327014
EST:     CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCG                         GCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
genomic: CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
EST: gi|162169895|gb|FC346251.1|FC346251
EST:     CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCG                         GCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
genomic: CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
EST: gi|7047392|gb|AW477286.1|AW477286
EST:     CCCAAAACACCTTCGTTCCCG                         GCGTAATTGAGTACGCTGTATAGAAGAAATCTCTTATTGGCGGTGATGACT
genomic: CCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
EST: gi|162241553|gb|FC418614.1|FC418614
EST:     CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCG                         GCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
genomic: CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
EST: gi|162221112|gb|FC397753.1|FC397753
EST:     CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCG                         GCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT
genomic: CGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACT

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: 43

GGAGAGAAAGAAATTTCGCCCTCTACCTTATTTGCTCTCGCTTGCATTCACGAACAAGTTCCATTCATCAATGGCAGCCCCCAAAACACCTTCGTTCCCGgtaagtgaaa ... tttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattccctcataaacttaacagtgcgtttatgtatatcgggaactttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT
              acttaac  putative branch site (score: 43)
                           tttatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgacttattcgagcatctgaaaccttgatgaggtctgcttccgaaaattccctcataaacttaacagtgcgtttatgtatatcgggaactttggtgcagGCGTAATTGAGTACGCTGTAGAGAAGAAATCTCTTATTGGCGGTGATGACTTCAAGAGCGGACAAACCAAGATGAAATCTGTGCTTGTGGACTTCCTCGT

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