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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtacctgatgtagtctagtcaaaggatagtaatatattttgtatactgtgtatagaatgatagctaaagaaatctcttgtttatgatag

Basic information

species Zea mays
transcript GRMZM2G116151_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 6
TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtac------------ctgatgtagtctagtcaaaggatagtaata-tattttgtatactgtgtatagaatgatagctaaagaaatctcttgtttatgatag
 ||| ||||||||||||| ||||| ||||||||||||||||| |||||| ||||||||||||| || ||||||||             |||||    ||| | ||  | |   ||||| | ||||| ||  ||  | | |||  ||||||||      ||||| |||||| |||
AATGTCTGTTGAAATGGTTGCTTGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaa------ctcttatttatgttag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 6
TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtacctgatgtagtctagtcaaaggatagtaatatattttgtatactgtgtatagaatgatagctaaag--aaatctcttgtttatgatag---------
 ||| |  |||||||||| || || |||||||| |||||||| || ||| | |||||||||||||| | |||||   |  | |      |   | |     |  | | ||| |||||  |   |     |  || |         | |||| |    ||             
GATGTCCATTGAAATGGTAGCATGTATTGCTATTGAAGCAATCTCTATATTAGAGAAGATGCACTCTAGAGGgtgagtactattaatctgcttatgatgcctgttttctttagtataaggaaaaagattttgtaccagggtttggacctctagagggtggacatgatttatc

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 6
TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtacc--tgatgtagtctagtcaaaggatagtaatatattttgtatactgtgtatagaatgatagctaaagaaatctcttgtttatgatag----------
|||| |  |||||||||| || ||||||||||| |||||||| |||||| |||||||||||||||| | ||||||    |  | |     |  | |   ||  |  |   || |   |  | | | |    |  |  ||   |   | | || || || |||           
TATGTCCATTGAAATGGTTGCATGCATTGCTATTGAAGCAATATCCATATTGGAGAAGATGCACTCCAGAGGgtaagaattttctgccacaaaccacaaattttgtttccttcttgtttttttttttttccttttttcttttgcgttttatt-ttaataatatgaaggatctt

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|101387539|gb|EB815784.1|EB815784
EST:     TGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG                         GTACGTCCATGGAGATGTGAAGCCTGAAAATTTTTTGCTTGGACC
genomic: TGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtacctgatg ... tttatgatagGTACGTCCATGGAGATGTGAAGCCTGAAAATTTTTTGCTTGGACC
EST: gi|71767696|gb|DR965633.1|DR965633
EST:     TGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG                         GTACGTCCATGGAGATGTGAAGCCTGAAAAATTTTTGCTTGGACCTCCAGG
genomic: TGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtacctgatg ... tttatgatagGTACGTCCATGGAGATGTGAAGCCTGAAAATTTTTTGCTTGGACCTCCAGG
EST: gi|78112677|gb|DV531071.1|DV531071
EST:     TGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGG                         GTACGTCCATGGAGATGTGAAGCCTGAAAATTTTTTGCTTGGACCTCCAGG
genomic: TGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtacctgatg ... tttatgatagGTACGTCCATGGAGATGTGAAGCCTGAAAATTTTTTGCTTGGACCTCCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCCTGTTGAAATGGTGGCTTGCATTGCTATAGAAGCAATTTCCATACTGGAGAAGATGCACTCAAAAGGgtacctgatgtagtctagtcaaaggatagtaatatattttgtatactgtgtatagaatgatagctaaagaaatctcttgtttatgatag

- - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG