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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggccattggctaccaaactgacttgatcatggcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG

Basic information

species Zea mays
transcript GRMZM2G010342_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 6
gttcctcacctcactgtgcattacctag---caaactggagcatgggcacaaggcaacacttggccatt--ggctac-caaactgacttgatcatggcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
      ||    |    |||||| | |    || | |        ||||||    ||    |||  |||     ||  | | || ||||||| || |||||||||||| || ||||| || || |||||||| ||||| || ||||||||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||||| |
------caaagaaaatagcattaacaaaacacagattcttctgcaggcacatttaaatgtctggttatttaaattattctagctaacttgattattgcatatgcagGTCTCGCTTTTAAATATCGTTGTTGAGTTGAAAAAGTGCTGCAACCACCCATTTTTATTTGAAAGTGCTGATCATGGTTATGGTGGAGATAGCATTGGTG

upper sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggccattgg-ctaccaaactgacttgatcatggcatatg-cagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
  |    |  | | |     ||   |  || | || |   |     | |    |   |     |   |  || |   || |  |  |  ||  | ||  ||||| || ||||| || ||||| || ||||| ||||| |||||||||||||| || |||||||||||||| || || || |||||||| ||        |  
actgacaaaattattagaagttttatttcataatgtatatttatttctatattattttctcttaaaagattatc--tctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA

upper sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
-gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggccattggctaccaaactgacttgatcatggcatatg-cagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
     || ||   | |  |       |       |   | ||      |          |   ||  |   | |  ||| |  |  |  ||  | ||  ||||| || ||||| || ||||| || ||||| ||||| |||||||||||||| || |||||||||||||| || || || |||||||| ||        |  
ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaaagatcatc--actaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA

upper sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
----------------------------------------------------------gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacac-ttggccattggctaccaaactgacttgatcatggcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
                                                           ||  || |  ||||||   |||  | |   | |  |  |||    | |      |  || |    |    | | |||   ||      |   ||   ||||| |||||||| ||||| || || || ||||||||||||||||| ||||| || || ||||||||||| || || || ||||| || || |  |  |   
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattattttaatatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA

upper sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 17
gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggccattggctaccaaactgacttgatcatggcata--tgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
     | | ||  |||   |   | |     |||   |  |   |      ||   | | |  ||||       |  |   |  ||| |  || |  ||||||| |||||| | || |||||||| |||||||||||||||||||| ||||| ||| | |||||||| || || || |||||||||||  | || | |  | 
--gatttaactttctgaataactcttgatttactcatggctattctttccccattccattgtaattgaactttgacatatatcaatcctttcaaaattgcagGTTTCACTTCTAAATATTGTTGTAGAATTGAAGAAATGCTGCAATCATCCTTTTCTATTTGAAAGCGCAGACCATGGTTATGGTGGGAACAGAAGTACCA

upper sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
lower sequence: PP1S93_123V6.1 (Physcomitrella patens), 3'ss of exon 18
------------gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggccattggctaccaaactgacttgatcatggcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
                 | |  ||  | |    | | |      ||   ||||   ||  | || | | ||   |  || ||    | || |  |            || |||| ||  |  ||||||| ||||| ||  | || || ||||| || ||||||||| |||||||||||||||| || || ||||||||||||   |      
actaccggttaaaactgtgatttctttttctgctgcttgtttttctcctgcattttcaagaagctaaagttttactgtgcctttttatctcatct------------tgtagGTTTCTTTGCTGAACATAGTTGTGGAGCTCAAAAAGTGCTGTAATCATCCATTTCTGTTTGAAAGTGCCGACCATGGCTATGGTGGAGATGCGAACATGA

upper sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
lower sequence: EFJ28029 (Selaginella moellendorffii), 3'ss of exon 16
gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggc--cattggctaccaaactgacttgatcatggcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
                                                  | |    || ||  | ||          |    |||| |        ||||||| || ||  ||||||| ||||| ||| | ||||| |||||||||||||| ||| | ||||| ||||| ||||| ||||| || | | ||   | |    
--------------------------------------------------gtatttttttgcgtcctttttcttttcgcatttttgaactcctaccttgcagGTGTCTCTGCTGAACATAGTTGTGGAACTAAAGAAGTGCTGCAACCATCCCTTTCTTTTTGAGAGTGCGGATCATGGTTACGGAGCAAATGCAACTATGA

upper sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
lower sequence: EFJ29460 (Selaginella moellendorffii), 3'ss of exon 16
gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggc--cattggctaccaaactgacttgatcatggcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
                                                  | |    || ||  | ||          |    |||| |        ||||||| || ||  ||||||| ||||| ||||| ||||| |||||||||||||| ||| | ||||| ||||| ||||| ||||| || | | ||   | |    
--------------------------------------------------gtatttttttgcgtcctttttcttttcgcatttttgaactcctaccttgcagGTGTCTCTCCTGAACATAGTTGTGGAATTAAAGAAGTGCTGCAACCATCCCTTTCTTTTTGAGAGTGCGGATCATGGTTACGGAGCAAATGCAACTATGA

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 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 95

ATACTACAAGTGGATTTTAGAGCGGAATTTCCAGAATCTAAATAAAGGAGTCCGTGGGAATCAGgtttttgtta ... gcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 82

ATACTACAAGTGGATTTTAGAGCGGAATTTCCAGAATCTAAATAAAGGAGTCCGTGGGAATCAGgtttttgtta ... gcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 83

ATACTACAAGTGGATTTTAGAGCGGAATTTCCAGAATCTAAATAAAGGAGTCCGTGGGAATCAGgtttttgtta ... gcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 69

ATACTACAAGTGGATTTTAGAGCGGAATTTCCAGAATCTAAATAAAGGAGTCCGTGGGAATCAGgtttttgtta ... gcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggccattggctaccaaactgacttgatcatggcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - -gtgcatt
- - - - - - - - - - - - - - - - ctggagc
- - - - - - - - - - - - - - - - - - - - - -gcacaag
- - - - - - - - - - - - - - - - - - - - - - - - - gcaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctacca