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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgctaacttaattagctgggtagaaacatctccagtgcaggcgaatacttttttagtttctccacgcttctttaataacaaactattttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAACTCGTGCAAGTTATGGGATTGGGCAAGACTCAACCTGACGAGATTCCGG

Basic information

species Physcomitrella patens
transcript PP1S4_12V6.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 2
ttgtgctaacttaattagctgggtagaaacatctccagtgcaggcgaatacttttttagtttctccacgcttctttaataacaaactattttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAACTCGTGCAAGTTATGGGATTGGGCAAGACTCAACCTGACGA-GATTCCGG
                         |    ||   |  ||  |   |||     |   | ||  ||  | ||  |  || ||      | ||  || |||||||||||||| ||||| ||||| || ||||||||||| || || || ||  | ||      |||||||||||||||  || ||||  | || ||  ||  
-------------------------gtcttattctct-tgttgattaatgtcagtcgtgatttgccttgatttgtggatgact-----tgttggatacagGAAGACTTCGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCTGAACCCCAAGATGAGCCCC-

upper sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 9
---ttgtgctaac-ttaattagctgggtagaaacatctccagtgcaggcgaatacttttttagtttctccacgcttctttaataacaaactattttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAACTCGTGCAAGTTATGGGATTGGGCAAGACTCAACCTGACGAGATTCCGG
   || | ||    || ||||    |  |   | | ||  |        |||| |   |   | ||  ||  | ||  |  || ||      | ||  || |||||||||||||| ||||| ||||| || ||||||||||| || || || ||  | ||      |||||||||||||||  |  ||||  | ||    ||  
gtcttattctcttgttgattaat--gccaaggatagctttaaatattctgaatgccagtcgtgatttgccttgatttgtggatgact-----tgttggatacagGAAGACTTCGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCCCAAGAAGAGCCCC

upper sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
ttgtgctaacttaattagctgggtagaaacatctccagtgcaggcgaatacttttttagtttctccacgcttctttaataacaaactatttt-atatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAACTCGTGCAAGTTATGGGATTGGGCAAGACTCA-ACCTGACGAGATTCCGG
  ||  ||  ||  |         | |  |   ||||    |   || |||   |  |    ||||| |||   |   || || | ||     || ||||||| ||||| || ||||| || || ||||||||||||||||| |||||||| || |||  |   |||||||| || ||  |  | ||  || | ||  |   
--gtcttatttttgtctaaccaagaaacgctattcca---taaatgattacaaataca---cctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC-

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|162178865|gb|FC354797.1|FC354797
EST:     TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAG                         GAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
genomic: TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
EST: gi|162159187|gb|FC334358.1|FC334358
EST:     TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAG                         GAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
genomic: TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
EST: gi|162175775|gb|FC352077.1|FC352077
EST:     TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAG                         GAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
genomic: TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
EST: gi|162198744|gb|FC374227.1|FC374227
EST:     TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAG                         GAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
genomic: TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
EST: gi|100406742|gb|BY955714.1|BY955714
EST:     AGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAG                         GAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
genomic: AGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
EST: gi|162185024|gb|FC362470.1|FC362470
EST:     TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAG                         GAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
genomic: TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
EST: gi|162187301|gb|FC363459.1|FC363459
EST:     GGAAAGCTCACTGTTGAATTGCGAACCCAAG                         GAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
genomic: GGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
EST: gi|162276463|gb|FC452466.1|FC452466
EST:     TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAG                         GAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA
genomic: TGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAA

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), 25 (downstream exon)
Score: 4

TTATGATGCACTGCATGGCGTTGCTGGTGTGTATGCTAAGAAGATTTTCTTGGAGGAATTGGGAGCGAAGGAAAGCTCACTGTTGAATTGCGAACCCAAGgtaagttcat ... ttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAACTCGTGCAAGTTATGGGATTGGGCAAGACTCAACCTGACGAGATTCCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatacttttttagtttctccacgcttctttaataacaaactattttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAACTCGTGCAAGTTATGGGATTGGGCAAGACTCAACCTGACGAGATTCCGG
                              taataac  putative branch site (score: 4)
                                        ctatttt  putative PPT
                         ttctttaataacaaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgctaacttaattagctgggtagaaacatctccagtgcaggcgaatacttttttagtttctccacgcttctttaataacaaactattttatatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAACTCGTGCAAGTTATGGGATTGGGCAAGACTCAACCTGACGAGATTCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA