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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattcttattgtagagcgacctttcattattgggtatatgtcagcaagtgaagtagttgtatcagtaggtgttgaactgatctgttcatcgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATG

Basic information

species Physcomitrella patens
transcript PP1S165_119V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G22320.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------gtattcttattgtagagcgacctttcatt----attgggtatatgtcagcaagtgaagtagtt-----gtatcagtaggtgttgaactgat-ctgt--tcatcgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATG
                                                                   |  || |  || |      |  ||| |||    ||    || |||||      |       ||     ||   || |  | | |   || |  | |  |  | | |||  ||||| ||||| ||||| ||||| ||| | ||||||||  | ||||||||||||||||| || ||||||||  ||  |  | |  |||||   || || || 
gtaacataccggattctccttcctcttttcttttttcttttttcccttccattttcaaatacctttagccttttatttttcattttattttttattttggataacataaatgtctttttttcttccttttccaaagtgaaaggaaatttagggttgttgttattgttgttgttttttagGGAGCAAGATGATTATGAGGTGGTGAGGAAGGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACGGACGGTGAGAAATGTGTCATT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G17520.2 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------------gtattcttattgtagagc---gacctttcattattgggtatatgtcagcaagtgaagtagttgtatcagtaggtgttga-actgatctgttcatcgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATG
                                                                                ||||  | ||| | |      |  |||  || ||   | |     || ||  |    | ||      || | |||||  | || | ||    |   |||  ||||| ||||| ||||| ||||| ||| | ||||||||  | ||||||||||||||||| || ||||||||  ||  |    |  |||||   || || || 
gtaacataacagattctccttcttcttttattgtttttccccccttcgattttcaaatacctttaaccttttttattttttatttattttggataatataaatgttttcttttttccttttccaaagtaaaaggga-atttagggttgttgttgttgttattgttgtgactctttttttttagGGAGCAAGATGATTATGAGGTGGTGAGAAAGGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 1
gtattcttattgtagagcgacctttcattattgggtatatg--tcagcaagtgaagtagttgtatcagtaggtgttgaactgatctgttca----tcgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATG
     ||| | |  |||  |  |      ||| | | | ||  ||  |||   ||    || || |  |   | |  || | |  |    |    |   ||||||| || ||||| ||||| ||||| ||||| || |||||  | |||||||| ||||| |||||||||||  | || | |   |  | |||||| ||  | || 
-----cttgt-gccgagttaattgatcgaatttgttctctgaatcctcaatataacctcttatacccttttctttaaaatttacttagcgagtattttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAGTGAAGTTTTTGAAGGCATAAATGTCAATAGCAATGAGCGCTGTATAATC

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|100439869|gb|BY980280.1|BY980280
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|208360006|gb|DC939310.1|DC939310
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|18351813|gb|BJ183865.1|BJ183865
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|18373505|gb|BJ205083.1|BJ205083
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100447198|gb|CJ971497.1|CJ971497
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|67709495|gb|BJ965311.1|BJ965311
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100397857|gb|BY990436.1|BY990436
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100422751|gb|BY957982.1|BY957982
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100386905|gb|BY988174.1|BY988174
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100401634|gb|BY954629.1|BY954629
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100436225|gb|BY979442.1|BY979442
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100360406|gb|BY984111.1|BY984111
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|18367245|gb|BJ199326.1|BJ199326
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100422530|gb|BY976419.1|BY976419
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|100390752|gb|BY971507.1|BY971507
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
EST: gi|67574586|gb|BJ947410.1|BJ947410
EST:     CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGG                         GGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG
genomic: CAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAG

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: 32 (upstream exon), 32 (downstream exon)
Score: 13

GACGGCCAGGTGTTATGTCCAAGGCCCGGGTTTACACAGATGTGAATGTCCAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttcca ... cgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtgaagtagttgtatcagtaggtgttgaactgatctgttcatcgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATG
                              aactgat  putative branch site (score: 13)
                                                tttcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcttattgtagagcgacctttcattattgggtatatgtcagcaagtgaagtagttgtatcagtaggtgttgaactgatctgttcatcgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa