Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagcctttctacacaattcaatcccctccacattccaagactgtgttagctgcaacttgaactcgccagcaattgctgcatgcagccctgacataacgtactttggatctttgtttgcag

Basic information

species Zea mays
transcript GRMZM2G141473_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141473_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g57680.1 (Oryza sativa), 5'ss of exon 9
TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagcctttctacacaattcaatcccctccacattccaagactgtgttagctgcaacttgaactcgccagcaattgctgcatgcagccctgacataacgtactttggatctttgtttgcag
|||||||||||||||||||| || ||||||||||| |||||||| ||||| ||||| |||||||||||||| || || ||||| |||||||| |||||||||||     ||        ||     |||       |  | |  |||   |    || | ||| ||   | |  ||  ||    |   | || ||                           
TGGACGTACAAGATCCCCACCGTGGACACCATCCCCAAGCAGTTCAACGTCGAGCTCATCAACAGCGCCCGCGATCACAAGCGCGTCCTCTCCTCCAAAGgtgaaatcatcg-------tcttcttcctttgagcactgaaatcgtgaagg----aaatcgaaatctgaaactgtt-ttgtgatccatcgtggcag--------------------------

upper sequence: GRMZM2G141473_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g57690.1 (Oryza sativa), 5'ss of exon 9
TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagcctttctacacaattcaatcccctccacattc-caagactgtgttagctgcaacttgaactcgccagcaattgctgcatgcagccctgacataacgtactttggatctttgtttgcag
|||||||||||||||||||| || ||||||||||| |||||||| ||||| ||||| |||||||||||||| || || ||||| |||||||| |||||||||||   | ||| |    ||   |||  |     ||| |||  |||  ||  |||  | |     | ||   |  |    ||||||||                                   
TGGACGTACAAGATCCCCACCGTGGACACCATCCCCAAGCAGTTCAACGTCGAGCTCATCAACAGCGCCCGCGATCACAAGCGCGTCCTCTCCTCCAAAGgtgaaaatctcttcttcgtttgctccttttttttttctcaaatctgaatt--ctgatattg----ttgctgtccttcatggcatgcag-----------------------------------

upper sequence: GRMZM2G141473_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g57720.1 (Oryza sativa), 5'ss of exon 2
TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgag--------cctttctacacaattcaatcccctccacattccaagactgtgttagct--gcaacttgaactcgccagcaattgctgcatgcagccctgacataacgtactttggatctttgtttgcag-----------------------------
|||||||||||||||||||| || ||||||||||| |||||||| ||||| ||||| |||||||||||||| |  || ||||| |||||||| |||||||||||         | | |       || |  |  |    ||     |  | ||   | |    | |||| ||| ||   | |  ||  |||   |   | || ||   ||| |  || | |       || |                             
TGGACGTACAAGATCCCCACCGTGGACACCATCCCCAAGCAGTTCAACGTCGAGCTCATCAACAGCGCCCGCGTTCACAAGCGCGTCCTCTCCTCCAAAGgtgaaatcatcgtcttcttcctttgatcctttttctcaaacgcatgagcaatgaaatcgtaaaggaactcgaaatctgaaactgtt-ttgcgatccatcttggca--gcgtccggtgaagccgccgccgctgctggcgtcgtcggtgcactgcgcgatgag

upper sequence: GRMZM2G141473_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os10g04860.1 (Oryza sativa), 5'ss of exon 9
TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagcctttctacacaattcaatcccctccacattccaagactgtgttagctgcaacttgaactcgccagcaattgctgcatgcagccctgacataacgtactttggatctttgtttgcag
|||||||||||||||||||| || ||||||||||| |||||||| ||||| ||||| ||||||| ||| ||  | || |  || |||||||| || ||||||||      | | | || |  |||  || |  |   |     | |     ||  | |||    ||||| | ||  || | | | ||||  ||   |   ||  || ||| |  |       
TGGACGTACAAGATCCCCACCGTAGACACCATCCCCAAGCAGTTCAACGTCGAGCTCATCAACACCGCTCGCCATCACAGCCGCGTCCTCTCCTCAAAAGgtga------caatataaatgcatcttctgctaacctc----ttcttcctcctcaatctttttttcgccgg-aacggcggaaggaagcc--gatcgatttta--ttagatttagg-------

upper sequence: GRMZM2G141473_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv18s0041g02390.t01 (Vitis vinifera), 5'ss of exon 8
TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagcctttctacacaattcaatcccctccacattccaagactgtgttagctgcaacttga--actcgccagcaattg-ctgcatgcagccctgacataacgtactttggatctttgtttgcag
||||| ||||||||||| ||||| |||||||| || |||||||| || |||||| | || |||||||  |   |  | || ||||| || ||||| ||||||     | ||| ||    |  ||        ||| | |    |||         ||||  |  | |        |||  || |     |  |  | ||||| |                     
TGGACATACAAGATCCCAACAGTTGACACCATACCCAAGCAGTTCAATGTTGAGATAATGAACAGCGGACAGCATAAAAAACGTGTTCTTTCTTCTAAAGgt--atttctcttcagctcttcattgaaaatgcatccta--gttgtagagaaaaaaactgaataattaatttctgattttcttcgactggaacaaatataacat---------------------

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|87153969|gb|DY398758.1|DY398758
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|5361195|gb|AI795615.1|AI795615
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|17921843|gb|BM259479.1|BM259479
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|37387457|gb|CF630922.1|CF630922
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|17921516|gb|BM259167.1|BM259167
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|88758370|gb|DY542739.1|DY542739
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|5005980|gb|AI712042.1|AI712042
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|5871449|gb|AW017920.1|AW017920
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|5296129|gb|AI783004.1|AI783004
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|5791471|gb|AI978263.1|AI978263
EST:     AGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTTTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: AGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|16925609|gb|BM078677.1|BM078677
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|47962486|gb|CN845195.1|CN845195
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|40335773|gb|CK369843.1|CK369843
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|17921574|gb|BM259225.1|BM259225
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
EST: gi|5895925|gb|AW037171.1|AW037171
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCT
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCT
EST: gi|16927116|gb|BM080185.1|BM080185
EST:     TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAG                         CATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA
genomic: TGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGA

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: 34 (upstream exon), 32 (downstream exon)
Score: 4

TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGAGGGAGGCCATCAGAGCCGCCAGGAAGGAATTCTCGGTCTGCACTGGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 785

TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGAGGGAGGCCATCAGAGCCGCCAGGAAGGAATTCTCGGTCTGCACTGGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 544

TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGAGGGAGGCCATCAGAGCCGCCAGGAAGGAATTCTCGGTCTGCACTGGTCC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 42

TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagccttt ... ttgtttgcagCATCCGGCGAGCCTCCGCTTCTTCTAGCTGCCTCGGTGCACTGCGCAATGAGGGAGGCCATCAGAGCCGCCAGGAAGGAATTCTCGGTCTGCACTGGTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACGTACAAGATCCCCACAGTCGACACCATCCCAAAGCAGTTGAACGTTGAGCTGATCAACAGCGCCCGTGACCAGAAGCGTGTCCTCTCTTCCAAAGgtgagcctttctacacaattcaatcccctccacattccaagactgtgttagctgcaacttgaactcgccagcaattgctgcatgcagccctgacataacgtactttggatctttgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC