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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtatcgctcaattcttgactcaggttcaggagcgaacgattgtgcttttccatgaaaatgccgtattagttattgtgtttgatttatgtcttgaagcaggttgttgtacaaggatgttagcctcctcgcatttcattacttaatctcttcctgctattgtagaaatatctctcgttattgttttgtag

Basic information

species Physcomitrella patens
transcript PP1S76_197V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 5
GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtatcgctcaattcttgactcaggttcaggagcgaacgattgtgcttttccatgaaaatgccgtattagttattgtgtttgatttatgtcttgaa-gcaggttgttgtacaaggatgttagcctcctcgcatttcattacttaatctcttcctgctattgtagaaatatctctcgttattgttttgtag
||  |  |||||||||| |||||||||||||| || || || || ||| | |||||||||||||||||||| || ||||         |||    |||  ||| |||    |   ||  ||  |     || | | | |    | |  ||||      |  ||| | | |  | || ||||                                                                                         
GCTATCCGGCGACGTTTTGACAAGCGTATCTATATTCCTCTCCCAGAGGCCAAGGCTCGGCAGCACATGTTCAAAgtat------tattca---tttgcttcaagtttctcaagtaaaaatcat-----tcaagggagaca--gaaccagtttactaatgagatctgttttgtaaatgcag-----------------------------------------------------------------------------------------
















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|162261190|gb|FC437207.1|FC437207
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162243142|gb|FC416742.1|FC416742
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162192379|gb|FC369087.1|FC369087
EST:     ACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: ACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162268434|gb|FC444203.1|FC444203
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162189691|gb|FC366329.1|FC366329
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTNTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162181630|gb|FC357932.1|FC357932
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162176272|gb|FC352729.1|FC352729
EST:     ACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: ACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162268433|gb|FC444202.1|FC444202
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162196818|gb|FC373886.1|FC373886
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162229089|gb|FC404773.1|FC404773
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162243141|gb|FC416741.1|FC416741
EST:     GAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|37846864|gb|BJ604872.1|BJ604872
EST:     TATCTACATCCCACTACCCGGAGTTTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACNTGACTGAACGTGATTATGAGGAT
genomic: TATCTACATCCCACTA-CCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|37853252|gb|BJ611260.1|BJ611260
EST:     TAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: TAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162187241|gb|FC363191.1|FC363191
EST:     ACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTNTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: ACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|37850914|gb|BJ608922.1|BJ608922
EST:     AAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: AAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162149983|gb|FC326514.1|FC326514
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|37825618|gb|BJ583684.1|BJ583684
EST:     TACCGGAGTNTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACNTGACTGAACGTGATTATGAGGAT
genomic: TACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|208397729|gb|DC911980.1|DC911980
EST:     GTATCTACATCCCACTACCGGANTCTANG-CTCGCCAGCACATGTTNANG                         -TGCATTTGGG
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGG
EST: gi|37824718|gb|BJ582784.1|BJ582784
EST:     AGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: AGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162269734|gb|FC445628.1|FC445628
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162196819|gb|FC373887.1|FC373887
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162169206|gb|FC345173.1|FC345173
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|37837980|gb|BJ595988.1|BJ595988
EST:     AAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: AAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|208350314|gb|DC925762.1|DC925762
EST:     GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: GTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
EST: gi|162154849|gb|FC331891.1|FC331891
EST:     ACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG                         GTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT
genomic: ACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGAT

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), 35 (downstream exon)
Score: 13

GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAGgtatgtgtat ... tgttttgtagGTGCATTTGGGAGATACGCCAAACAACCTGACTGAACGTGATTATGAGGATCTGGCTAGGAAGACTGATGGGTTTTCAGGCTCGGATATTGCAGTTTGT




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