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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA

Basic information

species Zea mays
transcript GRMZM2G110714_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 9
caggttgaaacataa-ccaagata-aaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
         |||||  | |||||| ||  | ||| || ||  |  |         || |||||   | || || |   |  |||   ||| |||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||   ||| |||| ||||| || |||||||||||  || |||||||||| |
-------gtacataggctaagatacaaaaaacttgcttactatgcta--------tacgtttt---ggttgtccttctggttgaaggtttcttcttttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGGTCTCTCTGTGCCTGTGGTGATAATTCTATTGCAGATGGCAGTCTTCTTGACTTTCTACGGCAAGTGTCCA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 8
---caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
          ||| || ||  |  |      |  |  |     ||||    |     ||     |   |     ||||  |     | ||| |||||||||||||| ||||||||||||| |  || || ||||| || ||||||||||||||  |  || | || ||||||||||| ||||| ||| |  ||||||| || |
tctgtcaaccaaatatgacttatttctcattttctcttgcaaattttaatctgatacataacacacaaaaa---gtctacaacctctatttattctcttgcagTTCCTGGAGCCTCTTGAACAATGCTATAGATCACTCTGTGCCTGTGGTGACAGACCTATAGCAGATGGAAGCCTCCTTGATTTCCTGCGGCAAGTTTCGA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 8
--caggttgaaacataaccaagataaag--gatctttctaaccgttttgggatatattatg-ttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
   |     ||| ||    ||    |    ||| |     | | ||||| || ||||  || | |||  ||| |        ||| |   | || |||     |||||||||| || ||||| |||||||||||||| || ||||| ||||| |||||  |  |||| |||||||||||||| || ||||| || ||||| || |
agaaaagaaaaaaatgtttaaaccgagactgatgtaatatatcattttgagagatatcttgatcttacagatacctaatcaaagtaaaattgttgtct-----agTTCTTGGAACCCCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGTGCAATTGCCGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 7
caggttgaaac-ataaccaagata--aaggatctttctaaccgtttt--gggatatattatg-ttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
 ||    |||  |||   ||  ||  || ||| |     | | ||||  | || ||||  || | ||    |  ||  ||     | |    || | |      |||||||||| || |||||||||||||||||||| || ||||| ||||| |||||  |  |||| |||||||||||||| || ||||| || ||||| || |
gagacaaaaaagatatttaaactagtaatgatgtgaaatatcattttctgagagatatcttgatcttccaaacactaatcatagttaaaatgttgtcc------agTTCTTGGAACCCCTTGAGCTCTGTTACAGATCACTCTGTGCTTGTGGCGATCGAGCAATTGCTGATGGAAGCCTTCTAGATTTCTTGAGACAAGTCTCTA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------------------------caggttgaaacataaccaa--gataaaggatctttctaaccgttttgggatatatt-atgtttta--tggat-tctcgtctcgagtgagtctt-------ttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
                                                                                   ||| |    ||   |    | | |  |  |||   |  | |   ||||  ||| |||||||   ||||| |||    | ||  ||  ||        ||   |  || ||||| ||||  ||||||| || ||||||||||| || ||||| ||||||||| |  |  |||| ||||||||||||||||| ||| | || ||||| || |
gtacatccattgcttttgctttcgtgtacttttccattaacacagttggggttttattatactgttgctagctatgtttttttgttaacttttagttatttaacatattagtttttggatggatcatggatgaatttatgttttccttggatatctttatttgacagacactaactaaagttaatttgtgtagTTCCTGGAATCTCTTGAACTATGTTACAGATCACTATGTGCTTGTGGTGATAGAGCAATTGCTGATGGAAGCCTTCTTGATTTCATGAGACAAGTCTCCA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G43050.1 (Glycine max), 3'ss of exon 7
-----caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
               ||| || | || |    || |||  |      |   |||||| ||  || |||  |  ||| | |    |    |  |||| ||||| ||||| |||||||||||||  | ||||| ||||| |||||||| |||||||| |   |  | || ||||||||||||||||| |||||  | ||||| || |
ataccttatgcatggcatgacaatgagactatatgttttcagaataatcatgatatagta-attatattaaaactc-tataacct---ccaattttttcttgtagTTCCTGGAGCCTCTTGAATTATGTTATAGATCGCTGTGTGCATGTGGTGACCAACCAATAGCTGATGGAAGCCTTCTTGATTTCTTGCGCCAAGTTTCCA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------------------------caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattc--tcgtctcgagtgagtcttttttctctt---gcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
                                                                        |     |   |  | |  || |   | | ||  |   ||||     |  || || ||    | ||||  | || |  | ||    ||| |||| ||   ||||||||||||||||||||||||||||||| |||| || ||| | ||||||||  || |  | || ||||||||||||||||| ||||| |||||||| || |
gtgagcaacctctatactctgaatttgttccttactaaattgtttcctgattttaacaacttgttagttcttgccattagagtttctatcattatccagccttacacttgtttccc--tcaataatattcacggaattcaattgtgtttactgttcttttattctatttatgcagTTCTTGGAGCCTCTTGAGCTCTGTTACCGATCACTATGTTCATGTGGTGACAGCCCGATAGCTGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCTA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G53310.3 (Arabidopsis thaliana), 3'ss of exon 7
caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
           || |     || | | |||||| ||||   |   || |||  | || |   |  |      ||||          |  |  |  || |||||||||| |||||||||||||||||| ||||||||||| | |||||||||||  |  | || ||||||||||||||||| ||||| |||||||| ||||
---------gtatcattgcaatta-gaatcttt-taac---tcccggttatgatttggtac-taaaccactctctca---------tgctatttgtgtagTTCTTGGAACCTCTTGAGCTCTGTTACCGATCTCTGTGTTCATGTGGTGATCGTCCAATAGCAGATGGAAGCCTTCTTGATTTCTTGAGGCAAGTCTCAA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 8
---caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtc--tcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
     | ||||| ||   | ||||| || | | ||  |    ||||   | |  |||   ||||||   ||     |  | || ||  ||| |||        |||| |||||||| |||||||| |||||||| || || ||||  || |||||  |  || |||| ||||||||||| ||||| |||||| | ||||||||||
atatggattgaaccact-ctaagatcaaagctgttgtt---tgtttcttgtttgattg-attttataattttctaacctttgattgtttctgtttctatccaaagTTTTTGGAGCCACTTGAGCTTTGTTACAGGTCGCTCTGTGATTGCGGTGACAGACCTATTGCTGATGGAAGCCTGCTTGATTTCTTACGCCAAGTGTCAA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 7
caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtctttt-ttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
||| ||| |   | |  ||  ||     | |||       |     | | |  | |||||    |  |   ||   || || |  || | || | ||| |||||||||| |||||||| |||||||||||||| || ||||| |||||||| ||  |  |||| |||||||||||||| || ||  | || |||||||| |
cagattgca-ttttattaatctaccattttttttcctttttgcatagttcttgtctgtttagctggattaggtactgattgggaattatatttttttgtagTTCTTGGAACCTCTTGAACTCTGTTACAGATCACTCTGTGCTTGTGGTGACCGACCAATTGCTGATGGAAGCCTTCTCGATTTTCTGAGACAAGTGTCCA

upper sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 7
caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagt--cttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
  | |     ||| | ||   |     || |   ||     | |    | || ||    || | | || |  | |  | |   |   |||| | |  || ||||| | ||||||||||| ||||| || ||||| || ||||| |||||||| ||  || |||| ||||||||||||||||| || ||  ||||||| || |
--gatgttttcattatcagattttgcaatttgcatagatagtgtatattttagtactgatttttgtttttttttttaaatttttaatttttattttctgtagTTCCTAGAGCCTCTTGAACTCTGCTATAGATCACTCTGTGCTTGTGGTGACCGGCCTATTGCTGATGGAAGCCTTCTTGATTTTTTGCGGCAAGTTTCTA

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: 49 (upstream exon), 49 (downstream exon)
Score: 215

CAGAGATAAACTCTATAACACACGTGAACGAGCACGTCACTTATTAGCTAGTGGGTTTTCTGAAATTCCAGAGGAAGCAACCTTCACCGATGTTGAACAGgtatgtaaag ... tctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 100

CAGAGATAAACTCTATAACACACGTGAACGAGCACGTCACTTATTAGCTAGTGGGTTTTCTGAAATTCCAGAGGAAGCAACCTTCACCGATGTTGAACAGgtatgtaaag ... tctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 92

CAGAGATAAACTCTATAACACACGTGAACGAGCACGTCACTTATTAGCTAGTGGGTTTTCTGAAATTCCAGAGGAAGCAACCTTCACCGATGTTGAACAGgtatgtaaag ... tctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 192

CAGAGATAAACTCTATAACACACGTGAACGAGCACGTCACTTATTAGCTAGTGGGTTTTCTGAAATTCCAGAGGAAGCAACCTTCACCGATGTTGAACAGgtatgtaaag ... tctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA
                                      tcttttttctcttgc  CT-rich tract
     tattatgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caggttgaaacataaccaagataaaggatctttctaaccgttttgggatatattatgttttatggattctcgtctcgagtgagtcttttttctcttgcagTTCTTGGAGCCTCTTGAGCTCTGTTACAGATCTCTGTGTGCCTGTGGTGATCGCTCTGTTGCGGATGGAAGCCTTCTTGACTTCTTAAGGCAAGTGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - -aaacata
- - - - - - - - -aagataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ttatgtt