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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGCTATCAAGGCGCTGACAGCTGTTATCAGACGCAGCCAGGCATCCACTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaaatgccgacagtctgttgcgtttactgaatagtttggataatactaaccttacaggtccaaatttgtgataagtcttgacagtctggttgggtgtatatgtgatcag

Basic information

species Physcomitrella patens
transcript PP1S96_37V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S96_37V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ19798 (Selaginella moellendorffii), 5'ss of exon 1
AGCAGCTATCAAGGCGCTGACAGCTGTTATCAGACGCAGCCAGGCATCCACTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaaatgccgacagtctgttgcgtttactgaatagtttggataatactaaccttacaggtccaaatttgtgataagtcttgacagtctggttgggtgtatatgtgatcag
 || || ||||||||||| || || || |||   |||||||| ||   ||| |||||||| |||||||| ||||||||||||||||| |||   ||||||||     |   | |   |     | |   || ||| |   |  |    | | |                                                               
GGCGGCGATCAAGGCGCTCACGGCGGTCATCCAGCGCAGCCAAGCCAGCACCATGATGGGCCTCGAGATCGAGCTCAAGAACGCCTCCGAGATGCTCAAGgttttcttgcttcctctcgcgtagctcacttcacttagctggatcttcactccag-------------------------------------------------------------

upper sequence: PP1S96_37V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ08630 (Selaginella moellendorffii), 5'ss of exon 1
AGCAGCTATCAAGGCGCTGACAGCTGTTATCAGACGCAGCCAGGCATCCACTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaaatgccgacagtctgttgcgtttactgaatagtttggataatactaaccttacaggtccaaatttgtgataagtcttgacagtctggttgggtgtatatgtgatcag
 || || ||||||||||| || || || |||   |||||||| ||   ||| |||||||| |||||||| ||||||||||||||||| |||   ||||||||     |   | |   |     | |   || ||| |   |  |    | | |                                                               
GGCGGCGATCAAGGCGCTCACGGCGGTCATCCAGCGCAGCCAAGCCAGCACCATGATGGGCCTCGAGATCGAGCTCAAGAACGCCTCCGAGATGCTCAAGgttttcttgcttcctcccgcgtagctcacttcacttagctggatcttcactccag-------------------------------------------------------------
















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|18350871|gb|BJ182922.1|BJ182922
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|67574689|gb|BJ947513.1|BJ947513
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|208352205|gb|DC906308.1|DC906308
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|208392681|gb|DC934011.1|DC934011
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|100443744|gb|BY963841.1|BY963841
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNN
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTT-
EST: gi|100386432|gb|BY951228.1|BY951228
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18329568|gb|BJ161574.1|BJ161574
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18366519|gb|BJ198598.1|BJ198598
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18355429|gb|BJ187488.1|BJ187488
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18359159|gb|BJ191219.1|BJ191219
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18329388|gb|BJ161394.1|BJ161394
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18343533|gb|BJ175571.1|BJ175571
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|208376907|gb|DC906848.1|DC906848
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG

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: 28 (upstream exon), 32 (downstream exon)
Score: 14

AGCAGCTATCAAGGCGCTGACAGCTGTTATCAGACGCAGCCAGGCATCCACTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTGCGGTATGTCACACGAACGACTGCACTAGAGTATGAGGACATTCGGGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGCTATCAAGGCGCTGACAGCTGTTATCAGACGCAGCCAGGCATCCACTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaaatgccgacagtctgttgcgtttactgaatagtttggataatactaaccttacaggtccaaatttgtgataagtcttgacagtctggttgggtgtatatgtgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC