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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaagcgtttgacgtcgatttggaggaaactcattaagaatactcgtgatcaaagtattaattcatgatgtggaattactgtgaacgaatggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGAAAGGGCAGTGTCAGGAG

Basic information

species Physcomitrella patens
transcript PP1S28_196V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G17880.1 (Arabidopsis thaliana), 3'ss of exon 1
---agaagcgtttgacgtcgatttggaggaaactcattaagaatactcgtgatcaaagtattaattcatgatgtggaattactgtgaacgaatggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGAAAGGGCAGTGTCAGGAG
       |  | |    |        |      ||||| |   |  | |  |   |  |    ||| |||   |    ||  | | |  |  |   | | |||||||| ||||||||| ||||||||||||||| | | || |||||||| |||||||| | |||||| ||
tttttgtgaatgtattattagcagttaatgtgttcattgattct-tttggaagtgatttggggattgatggattttgcttcttatta-tggtttataca-cagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG

upper sequence: PP1S28_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv17s0053g00620.t01 (Vitis vinifera), 3'ss of exon 1
agaagcgtttgacgtcgatttggaggaa-actcattaagaatactcgtgat------caaagtattaattcatgatgtggaattactgtgaacgaatggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGAAAGGGCAGTGTCAGGAG
     | |||    || |||||   | | | |   | |||| ||  |   |       | ||||  |||||||  |||    ||||  |   |        |  |||||||| ||||||||||| |||||||||||| ||||||||||||| ||||||||||| ||  | || ||
-----cttttacattcaatttgcctgtatatttcattagaagacctggattgccttgtatagtagaaattcatt-tgtatccttacactttcctctctttgtg-cagATGAATAGGGAGAAGCTTATGAAGATGGCTGGTGCAGTTCGCACCGGTGGAAAGGGTAGCATGAGAAG
















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|67568857|gb|BJ941681.1|BJ941681
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|7583801|gb|AW699705.1|AW699705
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|67508609|gb|BJ941471.1|BJ941471
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|67575201|gb|BJ948025.1|BJ948025
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|37824378|gb|BJ582444.1|BJ582444
EST:     TTCACTTCCCACCCCCCGGNTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: TTCAC-TCCCA-CCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|67698660|gb|BJ958893.1|BJ958893
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|162244341|gb|FC423814.1|FC423814
EST:     AGCTCTGCTCATCTTCACTCCCACCCCGGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|67576050|gb|BJ948874.1|BJ948874
EST:     GCTCTGCTCATCTTCACTTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: GCTCTGCTCATCTTCAC-TCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|162244340|gb|FC423813.1|FC423813
EST:     TCACTCCCACCCCGGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: TCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|18361165|gb|BJ193230.1|BJ193230
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|18345206|gb|BJ177247.1|BJ177247
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|67696648|gb|BJ956881.1|BJ956881
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|162201322|gb|FC376840.1|FC376840
EST:     AGCTCTGCTCATCTTCACTCCCACCCCGGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|67573263|gb|BJ946087.1|BJ946087
EST:     AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
genomic: AGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGA
EST: gi|67692062|gb|BJ952295.1|BJ952295
EST:     TCCCACCCCCGGGTCCTCAACAGCTTTTCCAAG                         ATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGG
genomic: TCCCACCCCCGGGTCCTCAACAGC-TTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGG

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: 29 (upstream exon), 35 (downstream exon)
Score: 39

CCTTTCCACTCAGTGTGCGTGTAAGTCTCGTGAGAAGATCCAAGCTCTGCTCATCTTCACTCCCACCCCCGGGTCCTCAACAGCTTTCCAAGgtgcgtgtgc ... ggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGAAAGGGCAGTGTCAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatcaaagtattaattcatgatgtggaattactgtgaacgaatggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGAAAGGGCAGTGTCAGGAG
          tattaat  putative branch site (score: 39)
      aaagtattaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaagcgtttgacgtcgatttggaggaaactcattaagaatactcgtgatcaaagtattaattcatgatgtggaattactgtgaacgaatggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGAAAGGGCAGTGTCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA