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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

Basic information

species Physcomitrella patens
transcript PP1S39_109V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
-tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgc-gggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
 |   ||||     | |  ||  ||       | |  | |  |  ||   | | |  | | | |||      ||| | ||||| ||||| | |  || |||||||||||||||||| || || || || ||||||||||| || || || || ||||||||||| || |||||||| || ||||| |||||||| || ||||
tttctcagtgaatctctgctgtagtgaactattattgtta-ttattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctg-acagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 2
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgca--cagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
             |   ||  |  ||  | |||| |||     || |  ||    || || ||  |    | |||||        || ||   ||    |||||||| |||||||| || ||||| || ||  |  | ||||| ||||| || ||||| || ||||| ||||||||||||||||||||||| ||||||||||
------------gtacaattttaatgcaacatcttttc-----ctttcagtattttttttggtcaactgaggtgatcatatttatatttcatgtgatgtcagGTTGTTGAGGATGGATATGAGTTCTTTGCCGACAGACAACTTGTCACCATATTCTCAGCTCCAAACTATTGTGGTGAATTTGATAATGCAGGTGCAATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 3'ss of exon 2
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgt---aggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
      ||   |  | |   |  ||    || || || |  |    |   | || |  |  ||| |   | || ||   ||    || ||          |||||||| || ||||| |||||||| || ||||| |||||||| || || || ||||| || || ||||| ||||| |||||||||||||| ||||| ||||
------gtgccccatgctcacaattacctgacctttttatttttcttaccaagtgaattgatttatcagttattcttgccttgttggaatt---------cagGTTGTCGAAGATGGGTACGAGTTCTTTGCTAACCGCCAACTTGTAACAATATTCTCGGCCCCTAATTACTGTGGAGAATTTGATAATGCTGGTGCCATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
                   |       ||  | | || | ||    |  ||  | |    | || ||||   |  || |   |  |||||        ||||||| |||||||| |||||||| || ||  |  |   | | || || ||||| || || ||||| |||||||| ||||||||||||||||||||  || 
-------------------gtaagcactaattattttgatctttattttgtctgttgagatctatataacaatt-tcagcatga-atgtctt-----tagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 3
-tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgat-ctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
 |  |   ||  | |||  ||| | |  |   |   |     |  |  |   |  | |     |  |   || | ||  ||   | |||||    |   |||||||| |||||||| || || ||||| ||| |  | || || ||||| || ||||| || || |||||||||||||||||||||||||| ||||||||||
gtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgt---cagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATATTCTCGGCCCCCAATTATTGTGGTGAATTTGATAATGCTGGTGCAATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G041822_T02 (Zea mays), 3'ss of exon 2
tgaccagttgtcttttcatg-ctgttggtagatctctt-cagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
  | ||  |    |   ||  ||||||     |   || ||  |   || |   |     ||  |    | ||    | |   | | || |  | | ||||||| || |||||||| || ||||||||||| || ||||| || || || || ||||| ||||| || || ||||| || ||||| ||||| |||||| |||
-aaacatctagagtgctatatctgttgagctgtgaattacaattttggttgtgcactgctttcattaccattgacttttttaactgaatctaactt-cacagGTCGTAGAGGATGGCTATGAGTTTTTCGCAAATCGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTTGACAATGCTGGTGCACTGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G02180.1 (Glycine max), 3'ss of exon 2
tgaccagttgtcttttcatgctgttggtagatctct-tcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtc---ccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
  |    |||    ||      | |  |   |||   ||   |    |   || |    | ||    | ||| |   || |     || |    |  || | ||||||| |||||||| ||||||||||| || ||||| || || || ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||
--atgtattgggcatttgcttggctcatcagtcttaatccattttaatgaattggtgaatctg-gttttatgttttcct-tctaaaattttgggctttgtatagGTTGTAGAGGATGGATACGAGTTTTTTGCCAAGCGTCAGCTAGTGACTATATTCTCCGCACCAAACTACTGTGGTGAATTTGATAATGCTGGTGCTATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G37370.1 (Glycine max), 3'ss of exon 2
tgaccagttgtctttt-catgctgttggtagatc--tcttcagctgctg-taggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
|   | | ||| ||   |||    ||||   |||  |||| | |   || ||  |  | ||   |||      |    |  | || |   |||        |||||||| |||||||| || |||||||| || ||||| || ||||| || || ||||| ||||||||||| || ||||||||||||||||| ||||| ||||
tatgctgatgtattgggcatttgcttggctcatcagtcttaatccattggtaaatctggtttaatgttttccttttaaaattttgggctttgtgttt----cagGTTGTAGAGGATGGATATGAGTTTTTTGCCAAGCGTCAGCTGGTGACGATATTCTCCGCACCAAATTACTGCGGTGAATTTGATAATGCTGGTGCTATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA03G41200.1 (Glycine max), 3'ss of exon 2
tgaccagttgtcttttcatgct---gttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
  ||      |   || ||| |    | ||  |||    |  ||  |  |    ||   | ||   |   |||  |  | |||    |   |    |   ||||||||||| ||||| |||||||| || ||||| || ||||| || || || || || ||||| ||||||||||| || ||||| ||||| ||||| ||||
-tactgtacatgcctttatgtttagatcgggggatag--taggcctcgatcaactatgctattgaaagtaaattgttttttgttttcggcctttttttaccagGTTGTGGAAGATGGATACGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAGTTTGACAATGCTGGTGCTATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
--tg-accagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatg-ctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
  || |||     |   || ||| | | | | |     |  ||  | |||   | |  |    | |  | |||   | || | |   ||   ||   | | ||||||||||| ||||| || ||||| || ||||| || ||||| || || || || || ||||| ||||||||||| |||||||| ||||| ||||| ||||
tttgtaccgtacatgcctttatgtt-tagatcgggggat--agtaggtgtcaatcaactatgctattgaaaataatttattttttttggccttcttttac-cagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G46820.1 (Arabidopsis thaliana), 3'ss of exon 2
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
         ||   | |||  | |   | | |  ||  || |  | |  ||| |     | | |  |  |||| |          |||  ||   |||||||||| |||||||| || ||||| || ||| |  | || || || ||||| || ||||| ||||| || |||||||||||||| |||||||||||| |||
---------gttagtacattgtataaat-gtttcctctagttttttt--gtttgggaaatcgaatctgctgctcaagaacctataatgctcc---cacagGTTGTAGAGGATGGGTATGAGTTCTTTGCTGATAGACAGCTTGTGACTATGTTTTCTGCTCCAAACTACTGTGGTGAATTTGACAATGCGGGTGCATTGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------tgaccagttgtctt--ttcatgctgttggtagatctc--ttcagctgctgt----aggttagattctttgtacataatgctgatctgtgcggga-tgtcccatgc--acagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
                                                                  ||||  ||| |||   ||||    |||   | |||     |||| || |      ||| |   |  ||| | ||  | ||  |  | | |   | | | |  | |   |||||||| || ||||| |||||||| || || ||| | ||||| || || || ||||||||||| ||||| ||||| || ||||| ||||| |||||| |||
gtaaagctaaaatttattccttgagttctctcttttgatttctctggattggtttgttcttctctgtgact-gttctctgaattcagagggttaagaaatcataactcagttgttaatgcaaggatctgtagttttttcaccaagccaagttttacttaactatactgttcctgcagGTTGTAGAAGATGGATACGAGTTCTTTGCAAAGAGACAACTAGTGACAATATTCTCTGCACCCAATTACTGTGGCGAGTTTGACAATGCTGGTGCATTGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv05s0049g00890.t01 (Vitis vinifera), 3'ss of exon 2
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccat-gcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
    ||| | | ||||   ||| || | |  | | ||  | |    |   ||| |    |    |||  | ||  |   | |    |  |   | |  ||||||||||| ||||| ||||||||||| |||||  | ||||| || || || || || ||||| ||||| |||||||| ||||||||||||||||| ||||
gtttcagctctgtttta--gctttttgcattttttttttggtcacct---ttaaacctctcaggcatttttctcttac-tacatatttccttgttgtgcagGTTGTGGAAGATGGATACGAGTTTTTTGCTAATAGACAACTTGTAACCATATTTTCAGCACCTAATTACTGTGGTGAGTTTGATAATGCGGGTGCCATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
                             | | |   ||    ||    |||  ||| ||| ||  | |||| | ||   |   | |   |  |   ||||||||||| ||||| || || || || ||  |  | || || || || || || ||||| || || ||||||||||||||||||||||| ||||||||||
-----------------------------gttattgccattcccttattgttccattttttataactcatgcagctcacagatagct--tctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA

upper sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv13s0019g02410.t01 (Vitis vinifera), 3'ss of exon 2
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatg-cacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
                   | | |||| |    | || || |       |||  ||| |       | |||||||    ||       ||   ||    |||||||||||||||| || || || || ||  |  | ||||| || ||  | ||||| || || || || |||||||||||||||||||| ||||||||||
-------------------gttattggca----tttttagttttctcttgttctattttac-----tcatgctgaaaactgaaattcttcttttggtctagGTTGTGGAGGATGGATATGAATTCTTTGCCGATAGGCAACTTGTTACCGTATTCTCAGCTCCCAACTACTGTGGTGAATTTGATAATGCTGGTGCAATGA

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|162168736|gb|FC344726.1|FC344726
EST:     CAGAGTTCTTACAAAAACATGACTTGGATCTCATCTGTCGAGCCCATCAA                         GTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATC
genomic: CAGAGTTCTTACAAAAACATGACTTGGATCTCATCTGTCGAGCCCATCAAgtactgtgat ... ccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATC




















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: 3

GGGAGACAATGACCGAGGTGTCTCTTTTACATTTGGTCCAGACACAGTCTCAGAGTTCTTACAAAAACATGACTTGGATCTCATCTGTCGAGCCCATCAAgtactgtgat ... ccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
                        tgctgat  putative branch site (score: 3)
                 tacataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

- - - - - - - - - - - - - - - - - - - - -tgctgta