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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGGTGCCATGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaaggtgagaattgtgaaatgaacatgtaggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaag...

Basic information

species Zea mays
transcript GRMZM5G899168_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G899168_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g56560.1 (Oryza sativa), 5'ss of exon 2
TTAGGTGCCATGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaaggtgagaatt--------gtgaaatgaacatg-----taggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaag
           ||  ||||||| |||||||| || ||||| |||||||||||||||||||| || |||||||| || | |||||||||||||||||| |  |||||||||||||||| |        ||   || | |||      | |||||   |||| | ||  |  ||| ||||  | |||| | ||||  ||||||      |  |||
----------CGAGAATGGCTCGTTTGATGCTGAACTCGAAATTGGATTCAAGTTCCTTGTCGAGAGTTATGTTTCTCATGTGGAGATGGAGAAGCCAAAATATATCAAGgtgagaacttcatcatggtactatcaccatactttattggttagtacataacataccatggaacacaagcatatctagaataactaaatggttc---tgaaag

upper sequence: GRMZM5G899168_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G04150.2 (Glycine max), 5'ss of exon 2
TTAGGTGCCATGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaaggtg---agaattgtgaaatgaac---atgtag--gttatg-gcataccttatgaatgaagacaataacatc-tggt-ataaggaaatggcctactttcaag
          |  |||||| ||||||||||| ||| | ||||||||||| || |||||||||||||||||||| || | ||| ||  |||| |  || | |  ||| |||||    |   |  |  | |  |    || |||  ||||    | |||||||||  || |  ||  |  ||| ||||  | ||    |   ||  ||     
----------TCCAGATGGATCATTTGATGCTGAGTTGGAGATTGGATTTAAATTCCTTGTTGAAAGTTATGTTTCTCATGTTGAATTGGACAGACCAAAGCGTATAAAGgtattcaacctcctctagtatatggtatttagtagttacctacttaccttatgcttgcattcaggaggatcatggttgtgagatttttttctggttgttg-

upper sequence: GRMZM5G899168_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G04320.1 (Glycine max), 5'ss of exon 2
TTAGGTGCCATGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaaggtgagaattgtgaaatga-acatg-taggttatggcataccttatgaatgaagacaataacatc-tggtataaggaaatggcctactttcaag--------
          |  ||| || ||||||||||| ||| | ||||||||||| || ||||| |||||||||||||| || | ||| ||  |||| || || | |  ||| |||||    |   |    ||  | ||| ||  || | |  |||||||||  || |  ||  |  ||| ||||     ||  |    |  ||             
----------TCCAGACGGATCATTTGATGCTGAGTTGGAGATTGGATTTAAATTCCTCGTTGAAAGTTATGTTTCTCATGTTGAATTGGACAAACCAAAGCGTATAAAGgtattcaacctcctctggtatatggtattttgtagt-taccttatgcttgcattcaggaggatcatggttgtcagatgttttttgattgttgctgttactt

upper sequence: GRMZM5G899168_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0038g00650.t01 (Vitis vinifera), 5'ss of exon 2
TTAGGTGCCATGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaaggtgagaattgtgaaatgaaca----tgtaggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaag-------
          |  |||||| ||||||||||| ||||| |||||||| || || || ||||||||||||||||| || | ||||||| |  | |  || | |  ||| |||||    |   ||   | |  |    |  || || |   ||          |   |  || |  |  |   || |   | ||      |||||         
----------TCCAGATGGATCATTTGATGCGGAGCTTGAGATTGGTTTTAAATTTCTTGTTGAAAGTTATGTTTCTCATGTGGAGTTAAACAGACCAAAGACTATAAAGgtagtgaagttggttttagaagttttacagtttttctgattttcccccctttttgttaacagaaaatta-atcaaatattgtttagttttcacaattaaaa

upper sequence: GRMZM5G899168_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv18s0001g10490.t01 (Vitis vinifera), 5'ss of exon 2
TTAGGTGCCATGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaaggtgagaattgtgaaatgaacatgtaggttatggca----taccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaag------
          |  |||||| ||||||||||| ||| | |||||||| ||||| || |||||||||| |||||| |||| ||||||| |  | | ||| | ||  || ||||| |        |  |  |  |||  ||| | | |    ||   |   | |||      |    | |    | |  | |  | | | |    |       
----------TCCAGATGGATCATTTGATGCTGAGTTGGAGATTGGTTTCAAATTTCTTGTTGAAAATTATGTTTCCCATGTGGAGTTAAACAGGCCAAAGTGCATAAAGgtaattgactcaatttctagctgtttgttttagaagtaataaagtgatattgattttttttttctttttggttaatagaaagtcaattgaagaatgttca

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|113703127|gb|EE680631.1|EE680631
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAG-CC--------C-AGgtatatcaag ... c
EST: gi|211244285|gb|FL461030.1|FL461030
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAG                         ACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaag ... ctacatgcagACTACAGCATCTGAAAGTGGACTTTTTGATCATTTGGTAAACGTTTGGGAG
EST: gi|211064849|gb|FL464106.1|FL464106
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAG-CC--------C-AGgtatatcaag ... c
EST: gi|14244480|gb|BG842515.2|BG842515
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAG-CC--------C-AGgtatatcaag ... c
EST: gi|74232388|gb|DT640302.1|DT640302
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAG                         G
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaag ... ctacatgcag-
EST: gi|74232388|gb|DT640302.1|DT640302
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAG                         G
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaag ... ctacatgcag-
EST: gi|74232388|gb|DT640302.1|DT640302
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAG                         G
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaag ... ctacatgcag-
EST: gi|37373856|gb|CF623251.1|CF623251
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAG-CC--------C-AGgtatatcaag ... c
EST: gi|74232387|gb|DT640301.1|DT640301
EST:     AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGGTATATCAAG                
genomic: AAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAG-CC--------C-AGgtatatcaag ... c

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAGGTGCCATGAAGATGGCTCATTTGATGCAGAGCTCGAGATTGGATTCAAGTTCCTTGTTGAAAGTTATGTCTCCCGTGTGGAGATGGAGAAGCCCAGgtatatcaaggtgagaattgtgaaatgaacatgtaggttatggcataccttatgaatgaagacaataacatctggtataaggaaatggcctactttcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaaat