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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT

Basic information

species Physcomitrella patens
transcript PP1S165_119V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 3
---ttttaaaattcttcctatcttggtttgcc-attcctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
      |     |  | |  | || ||      | |    |  |||||||   |  ||| ||     || |   |      | | | |    | |   || ||||| ||||| || || ||||||||||| ||||||||| | ||||| ||||| ||||| || |||||||||||||| |  || |||||| |  | ||||| |
attcagttgggcttgttcggtgttcgtcgatttagtagccaggacttatttctaatctcctgtt---atcttttttctaaattccgtcctgcttacc-ttccagGCATTGGATTACTGTCATTCTCAAGGAATTATGCACCGCGATGTCAAGCCTCACAATGTTATGATTGACCATGAACTCCGCAAGCTTCGCTTAATTGATT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 3
-------ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
        | ||  |   | |   || |   | |       | |  | || ||  |  |  ||   |  |||||||       || |||  |     || | |||||||||| || || |||||||| ||||| || |||||| | ||||||||||| ||||| || ||||| || || ||||  || || ||  |  | || ||||
ttttcttctataggagaatccaagtcatacatcgtttggtttgagcaatttttggctgatccaattat-gatataa-cacccttttctgttg-----atgggtgcagGCTTTAGATTACTGCCATTCACAAGGCATCATGCACCGCGATGTGAAGCCTCACAATGTTATGATAGATCACGAGCTTCGAAAACTCCGATTAATAGACT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 3
ttttaaaattcttcctatct--tggtttgccattc-ctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggagtcatt--gttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
    |  |     || |  |  || |   | | ||   ||||| ||||||    ||      || ||  |  |  ||  | ||||     ||  |   | | ||||| || || || |||||||| ||||| ||||||||| | ||||||||||| ||||| || ||||| || |||||||  ||||| ||  |||| || ||||
--aaatgaccacaccaagttactgctgaacaagtcatcaacaaattattaaggaacct---tagtgagtttgacttgcctaactgtttttgttctctggatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCCCACAATGTTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 3
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagagatataaatgtgggt-tactgacggagtcattgtt--------gcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
    |  | | ||  | ||     ||  ||     |  ||| | |  |   | |   |  |  || | | | ||| |  | | || |  ||  | ||         ||||| || || || |||||||| ||||| ||||||||| | ||||||||||| ||||| || ||||| || |||||||  ||||| ||  |||| || ||||
----agcagtttttttttccctaattatca-----aggaacctgtgtttgcaattgagtgggaatttcactatggttgcattaactgtttctgttttctggatatacagGCATTAGATTACTGCCATTCACAAGGTATTATGCACCGAGATGTGAAGCCCCACAATGTTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 3
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagaga-tataaatgtgggttactgacggagtcattg--ttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
   | |  | |||                ||| ||||  | ||      ||    ||| |||   | |   |||    |    ||       |||  |||||||||||||| || |||||||||||||| |||||||| |||||||| ||||| || || || ||||| || ||||||   || || ||| |  | || || |
---tcatttgcttatgtatccacaaaattattactaaatatttgagcaaatgtgtatggagaacctttccttgttacctgaatactttagtgttgaattgcagGCTTTGGATTACTGCCATTCTCAAGGCATTATGCATAGGGATGTCAAGCCTCATAATGTCATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G17520.2 (Glycine max), 3'ss of exon 3
--ttttaaaattcttcctatcttggtttgccattcctaacaacttattat-catactcatgcagagatataaatg-tgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
   | || | ||     ||  ||  |||  || ||| | ||  |  |  | | |     |    |  |  ||  | |  |||| |   ||| |   ||   |||||  |||| ||||||||||| ||||| || |||||  | |||||||| ||||| || || |||||||| ||||||||||| |||||| | ||||| || |
ggatctatagtttgcattaaattattttttcaatccaaccatttcgtattgcttgtggctatcaacttggaagcgctaagttatt--tggaatttctgc--cagGCACTGGATTATTGCCATTCACAAGGAATCATGCATCGTGATGTGAAACCACATAATGTAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G22320.1 (Glycine max), 3'ss of exon 3
--ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
   | || ||||     ||  ||  |||  || ||| ||| | ||  |||           |   |  |  | | |      | |  |     || |  |||||  |||| ||||||||||| ||||| || |||||  | |||||||| ||||| || || |||||||| ||||||||||| |||||| | ||||| || |
tgatctataatttgcaatagattattttatcaatcc-aaccatttcctattgcttgtggctatcaacttggaagcgctaagttaattggaa-gttctgccagGCACTGGATTATTGCCATTCACAAGGAATCATGCATCGTGATGTGAAACCACATAATGTAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcat-gcagagatataaatgtgggtt-actgacggagtcattg-ttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
   | |  | ||||        |      ||| ||||  | ||      ||    || |   |  | |  ||||    | | ||    |||  |   |||||||| ||||| || |||||||||||||| || ||||| |||||||| ||||| || || || ||||| || ||||||   || || ||| |  | || || |
---tcatttgcttctgtatccagaaaattattactaaatatttgagcaaatgtgtattgtgaacctttccatgttacctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 4
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT--------------------------------------
                     | |  | |  | |   | |        |        |||   ||   |||      | |||||  | ||     |||   | |||     |   ||||| |       |    |||| || |||||||| ||||||||||||||||||||     ||||| ||||  |||| || ||||                                      
--------------------agatcaggcgatgc--gcgaggcgacgcctggagtgcgcaacaatgccaat-caacctcctgacataatc-----tgc---ccttgt----tcatcattcccgccatgct---tacagAGACGTGAAGCCGCACAACGTGATGATTGACCACTCCAAGCGGCAGCTGCGGCTCATAGACTGGGGCCTGGCGGAGTTCTACTTCCCGGAGCGCGAGTTC

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ28543 (Selaginella moellendorffii), 3'ss of exon 3
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggag-tcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
                                       |  | || | |  | ||||  ||         |  || |  ||| |  | |  || ||||||||  | ||  | ||||| || ||||| |||||||||||||| |||||||| ||||| ||||||||||| || |||||||| |||||  | || || ||||
------------------------------------gtgaggtttt-ttaaccccatgtggattggacttgggaggattttgatgttgcttgtttttgcagGCACTCGATCACTGCCACTCGCAAGGAATTATGCACAGGGACGTGAAGCCGCACAATGTGATGATTGATCACGAGCAGCGCAAGCTGCGCCTCATCGACT

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 3
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagag-atataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
                                       |  | || | |  | ||||  ||    |     | || ||     |    |  || ||||||||  | ||  | ||||| || ||||| |||||||||||||| |||||||| ||||| ||||||||||| || |||||||| |||||  |||| || ||||
------------------------------------gtgaggtttt-ttaaccccatgtggattggacttgggaggattttgatcttgcttgtttttgcagGCACTCGATCACTGCCACTCGCAAGGAATTATGCACAGGGACGTGAAGCCGCACAATGTGATGATTGATCACGAGCAGCGCAAGCTGCGGCTCATCGACT

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|208360006|gb|DC939310.1|DC939310
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAAGGGATTATGCACANGGATGTGAAGCCA
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCA
EST: gi|100447198|gb|CJ971497.1|CJ971497
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAAGG-ANTATGCACAGGGATGTGAN-CCA
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCA
EST: gi|162267952|gb|FC444033.1|FC444033
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCA
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCA
EST: gi|67709495|gb|BJ965311.1|BJ965311
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATT
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATT
EST: gi|100397857|gb|BY990436.1|BY990436
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTNCA-GGGATTATGCACAGGGATGTGAAAGC
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCT-CAAGGGATTATGCACAGGGATGTGAA-GC
EST: gi|100401634|gb|BY954629.1|BY954629
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGCGAAGCCA
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCA
EST: gi|100436225|gb|BY979442.1|BY979442
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAGGGGAT
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGAT
EST: gi|67574586|gb|BJ947410.1|BJ947410
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTC
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTC

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), 34 (downstream exon)
Score: 7

CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatactcatgcagagatataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
                                tactgac  putative branch site (score: 7)
                agatataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcatgcagagatataaatgtgggttactgacggagtcattgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - ctcatgc