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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatctggaataaaatttggctctgttgccgcgatgttgattcgattgactcaccgttcataaagtattgaattagttttcttttgtctcttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGCTTTTGAATATTCAGCGAGGCATGGACTTGAATGGTGGCAGCTAGACCCA

Basic information

species Physcomitrella patens
transcript PP1S495_13V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S495_13V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G22730.1 (Glycine max), 3'ss of exon 4
tgatctggaataaaatttggctctgttgccgcgatgttgattcgattgactcaccgttcataaagtattgaattagttttcttttgtctctt-cattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGCTTTTGAATATTCAGCGAGGCATGGACTTGAATGGTGGCAGCTAGACCCA
              ||||   | | || ||   |   |       |||       |||       |  |  ||   || |  |   |       ||   |||||||||||  | ||||||||||| || ||||||||||||||||| ||||||||||| || ||||| || ||||||||||| ||||||||  |||||   
------------gtattttttttttttaccttaaacatttcatagttggtaattggtttgagtttttatatatacattataatccattgaaaatatcttagGTGGGTGGCGTTGCTTGCATTTGGTGAGGGTTGGCACAATAACCACCATGCTTTTGAGTACTCAGCTAGACATGGACTTGAGTGGTGGCAAATAGACATG

upper sequence: PP1S495_13V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G03370.1 (Glycine max), 3'ss of exon 5
tgatctggaataaaatttggctctgttgccgcgatgttgattcgattgactcaccgttcataaagtattgaa-ttagttttcttttgtctcttcattgc--agGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGCTTTTGAATATTCAGCGAGGCATGGACTTGAATGGTGGCAGCTAGACCCA
      | | |    |||  |  |         ||  |      ||||  |    ||||| ||  |||||   ||| | |    |    ||   ||| |  |||||||||||  | ||||||||||| || ||||||||||||||||| ||||||||||| || ||||| || |||||||| || |||||||| ||||||   
------gtattttttttttaccttaaatttttcatagtttagtaattggtttga-gttcacaagttattgttcttaatatataatccattcaaaatttcttagGTGGGTGGCGTTGCTTGCATTTGGTGAGGGTTGGCACAATAACCACCATGCTTTTGAGTACTCAGCTAGACATGGACTAGAGTGGTGGCAACTAGACATG

upper sequence: PP1S495_13V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0002g06970.t01 (Vitis vinifera), 3'ss of exon 4
tgatctggaataaaatttggctctgttgccgcgatgttgattcgattgact-caccgttcataaagta-ttgaattagttttcttttgtctcttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGCTTTTGAATATTCAGCGAGGCATGGACTTGAATGGTGGCAGCTAGACCCA
          |||   |   | ||| | |    ||  | | || |    || | | | ||  ||| |  | | | | ||||  |||   ||      | ||||||||||| | | |||||||| ||||| || ||||||||||| || |||||||||||||| || ||  | ||||| || |||||||||||  | ||    
---------gtaaggctc--ccctgcttctaaaattctaagtctaccctctaccctggtctgaaactggtcgtaattgtttgatttgaacttgggtgttcagGTGGGTGGGATTGCTTGCATTCGGAGAGGGGTGGCACAATAATCACCATGCTTTTGAATACTCCGCTCGTCATGGCCTGGAATGGTGGCAAATTGATATG

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|162171756|gb|FC348425.1|FC348425
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|162187131|gb|FC362913.1|FC362913
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|208365510|gb|DC954751.1|DC954751
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|37850729|gb|BJ608737.1|BJ608737
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|37833193|gb|BJ591205.1|BJ591205
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|67699657|gb|BJ959890.1|BJ959890
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGA-TTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|162231669|gb|FC408262.1|FC408262
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|162231668|gb|FC408261.1|FC408261
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|162171757|gb|FC348426.1|FC348426
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAG
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAG
EST: gi|162195065|gb|FC368779.1|FC368779
EST:     GTTTGGGGCTCACAAAAGTGGAATGCGGGTGATTTATCAAGGAATAAGTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|37851278|gb|BJ609286.1|BJ609286
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|37830486|gb|BJ588498.1|BJ588498
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|18335242|gb|BJ167260.1|BJ167260
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
EST: gi|162195066|gb|FC368780.1|FC368780
EST:     GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTG                         GTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC
genomic: GTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGC

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), 33 (downstream exon)
Score: 8

GAGTTGTGTGGGTCTATCACATTACGTGGTTTGTGAACTCAGCATCTCATGTTTGGGGCTCACAAAAGTGGAATACGGGTGATTTATCAAGGAATAACTGgtaaatttgt ... ttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGCTTTTGAATATTCAGCGAGGCATGGACTTGAATGGTGGCAGCTAGACCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactcaccgttcataaagtattgaattagttttcttttgtctcttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGCTTTTGAATATTCAGCGAGGCATGGACTTGAATGGTGGCAGCTAGACCCA
  gactcac  putative branch site (score: 8)
                               ttttcttttgtctctt  putative PPT
              ataaagtattgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatctggaataaaatttggctctgttgccgcgatgttgattcgattgactcaccgttcataaagtattgaattagttttcttttgtctcttcattgcagGTGGGTGGCACTTCTTGCATTTGGAGAAGGTTGGCACAATAACCATCATGCTTTTGAATATTCAGCGAGGCATGGACTTGAATGGTGGCAGCTAGACCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT