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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgctgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatctttctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATTTTAGGTC

Basic information

species Physcomitrella patens
transcript PP1S28_307V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 2
gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgctgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatctttctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATTTTAGGTC--
                                            | || | ||  |||||  |       |  | |  ||   |  |||  |||  ||  |   |  |||  |||    ||  ||| || |  | |  || |||     ||||||||||||||||||||| ||||| | ||||||| | | ||||  ||||       |||  |    ||| | |||||||  |||||   |||   | | |   
--------------------------------------------caca-actgttactgttgccaaattttcatctccacagcatcttgagatgc-atattgttt-cttgctcttaaactgaccttttgctttgac-catgttt-----gcagATGGACCCCAAGTTCCTGAGGAACCTGAGGTATTCTAGGAAGGGCAACAAAAAGAGTGGTGAGGCTGAAGCTGAGGAGTAGGAAGG--AAAGCATGGCTTTG

upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 2
gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgctgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatctttc-tgtg-gcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATT--TTAGGTC----
                                                       |||||  ||| | ||   | |  | ||   |  ||  || | ||| | | |  |    || || |   |  ||||        ||    | |||  ||||||||||||||||||||| ||||| | ||||||| | | ||||  ||||  |    |||      |||||| |||||||  |||||   |   |  ||  ||     
----------------------------------------------------acaactgttacttttgccaatttttcatctctaacagc--tgct-tgagatgcaccttggtttttgctctacaactgaccctttgcattgaccatgtttgcagATGGACCCCAAGTTCCTGAGGAACCTGAGGTATTCAAGGAAGGGCAACAAGAAGAGTG------GTGAGGCTGAGGAGTAGGAAGGAAAGCATGGTTGTGTTTCCT

upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 2
------gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgc-tgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatcttt-----ctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATTTTAGGTC
       |   | | ||  | ||| ||| | |      || | ||  |      |  |  |  |    ||  ||| |   | | |   ||     | ||| | || || | | ||| |||            | |    |    | |  ||      ||  | ||||||| |||||||| || |||||||||||||| |||| ||||||||||  |    |||  |  |  |     |||||   |  | |    | |||    |
gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC

upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G04280.2 (Glycine max), 3'ss of exon 1
---------gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgc-tgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatcttt-----ctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATTTTAGGTC
          |   | | ||  | ||| ||| | |      || | ||  |      |  |  |  |    ||  ||| |   | | |   ||     | ||| | || || | | ||| |||            | |    |    | |  ||      ||  | ||||||| |||||||| || |||||||||||||| |||| ||||||||||  |    |||  |  |  |     |||||   |  | |    | |||    |
gtagtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC

upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G06700.3 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgctgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatctttctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAAT-TTTAGGTC-----
                                                  || |  || |   ||  |  |      || || |  |   | |    | ||| || || ||  ||   ||  |    | ||  |  ||    ||      ||||||||||| |||||||| ||||| |||||||| || | ||||||||||      |    |||| | |||  ||      | ||||| ||| | ||| | |      
--------------------------------------------------gtaagtctct-tattacagttctaacctaactgatttcagattcgggttata-gtgttggaggtttgattattgcgtttatgtgaaatgatgttt-----cagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAAC------GTCAAGGCCGGCGAGAATGCTAGCGCTGAAGAATAAGTGTTTTGATTATCTG

upper sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv05s0077g01220.t01 (Vitis vinifera), 3'ss of exon 1
gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgctgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatctttctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAG--ACGGAAGAGTAAATTTTAGGTC
                                                  || |        |||  |  | || | | ||   | ||    ||  |  ||| ||  ||||   |  | ||   || || |  |  | ||||        ||||||||||| |||||| | ||||| |||||||| |||| ||||||||||  |    | |  |     |     |||||   |  ||  |  ||   |||||  
--------------------------------------------------gtaatttctcaactttgatttactcttttccccccttttttctga-agaatatgtgattga---tgcgatgaatttgtgttttg--aaatctgaaatgaacagATGGACCCGAAGTTCTTGAGGAACCAGAGGTACGCGAGGAAGCACAACAAGAAGAGCGGTGAATCCGCCACCGAGGAAGAATAGACCAACAATGATTAGG--

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|162230925|gb|FC407180.1|FC407180
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|7147989|gb|AW509911.1|AW509911
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|6167331|gb|AW145595.1|AW145595
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|7287274|gb|AW599761.1|AW599761
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|67694976|gb|BJ955209.1|BJ955209
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|15730019|gb|BI741618.1|BI741618
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|18352170|gb|BJ184224.1|BJ184224
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|7047097|gb|AW476998.1|AW476998
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|37827441|gb|BJ585453.1|BJ585453
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|18338608|gb|BJ170632.1|BJ170632
EST:     AGGATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|7207648|gb|AW561588.1|AW561588
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|18348071|gb|BJ180118.1|BJ180118
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|18346549|gb|BJ178594.1|BJ178594
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|67571625|gb|BJ944449.1|BJ944449
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|18358137|gb|BJ190196.1|BJ190196
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|37831859|gb|BJ589871.1|BJ589871
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|67569327|gb|BJ942151.1|BJ942151
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|37825658|gb|BJ583724.1|BJ583724
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|67692587|gb|BJ952820.1|BJ952820
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
EST: gi|7583117|gb|AW699281.1|AW699281
EST:     AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGG                         ATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG
genomic: AGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGG

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), 35 (downstream exon)
Score: 19

GGCGAAATCTAAGAATCATACCGCTCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTGAAGAAGCACAAATATGCCTCAAGGAAGGGGgtgagtatat ... tctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATTTTAGGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacgtatttgaacttctgttgctcttctgatagggcatatctttctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATTTTAGGTC
                          ttctgat  putative branch site (score: 19)
                                       tatctttct  putative PPT
      tatttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgctgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatctttctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATTTTAGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA