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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag

Basic information

species Zea mays
transcript GRMZM2G166035_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 5'ss of exon 6
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag
|||| ||| | || ||||| ||||| ||||| |||||||||||||||||||| || ||||||| |||||| |||||||| || || ||||||||||| | |   || ||   ||  || |  | |     |   | | |    || |||  ||   |    | ||| |||        |      | |   |||                                                                                     
GGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGgtttgacttaatttgtttgcttagctctcaactaa--agccttctatctgcaaaataatattcatcatcgtaat-tggcattcccatgcatgttactctaaag------------------------------------------------------------------------------------

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G06250.1 (Glycine max), 5'ss of exon 7
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag
| || |||||||| || || ||||| ||||| ||||| ||||||||||||| |||| |||||| ||||||||||||||| || |||||  |||| ||||    | | | |||  |    |  ||| | || |||| || |  |   ||    |  | | |  |  | || | | | |    |  |||  |||                                                                                       
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtc---tactatggttagttacgtccatt-cttgaatatcttatatagttatggattcatctca--acctgtgct-catatagggtgcatggttaagtgtaca--------------------------------------------------------------------------------

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA14G12220.1 (Glycine max), 5'ss of exon 6
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttt-tgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttg---taataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag
| || |||||||| ||||| ||||| ||||| || || ||||||||||||| |||| |||||| ||||||||||||||| || |||||| |||| |||     || |  ||  |  | | | |  |   |  |||| || |  | ||  |||    | || |    ||| |   |  ||   || || |||  |                                                                                         
GAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAGgtgtgtttctaatatggtgaatccattcttggatatttc-atatattctt-agactcatctcaatctgtgtctgtatagattgcatgacttagtatatggtt-----------------------------------------------------------------------------------------

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G06310.1 (Glycine max), 5'ss of exon 6
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag
| || |||||||| || || ||||| ||||| ||||| || |||||||||| |||| |||||| ||||||||||||||| || |||||  |||| ||||    |   | |||  |   ||  ||| | || |||| || |  |   ||    |  | | |  |  | || | | | |    |  | |  | | |   |                                                                                 
GAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAGgtatgtc---tacaatggttagttacatccatt-cttgaatatgttatatagttatggattcatctca--acctgtgct-catatagggtgcacggttcacatttgt--------------------------------------------------------------------------------

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 7
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatg-gtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag
| || |||||||| ||||| ||||| ||||| || || ||||||||||||| |||| |||||| ||||||||||||||| || |||||| ||||   |  |  | | | ||   | | ||  ||| | |||||||||    || | ||     | ||      ||| || ||  || |  | |  |||  | |  |                                                                                    
GAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAGgtgcatt-tctaatatggtgaatccaatccatt-cttggatattt----catatattcttagattcagatgaatctgtgtctgtatagagtgcatgatttagtata----------------------------------------------------------------------------------

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 5'ss of exon 7
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgt---ttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag
| ||||||||||| || || ||||| ||||| ||||| |||||||| ||||   | ||||||| ||||||||||||||| || || ||  |||| |          |   ||||| | |     | |    |||| ||    ||| ||  ||   | | |  ||  || |  | |    || | |  ||  | | |    |  |                                                                              
GAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAGgtat----------tgactttttgccaaaatctcctcctatatatt----aaaaatgccactttgttattaacaattgaacataacctgcattggatttcaatagttagctact----------------------------------------------------------------------------

upper sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 7
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag
| || ||||| || || || ||||| ||||| ||||| ||||||||||||| ||||||||||| ||||||||||||||| || |||||| |||| ||            | | | |   | ||| |    | || ||       |||||   ||  |  ||  ||| |  |||  ||  |||  || || |     ||| |  ||    || |||   |                                                            
GAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAGgtctg------------gctctgagagttgatagtaaagctagtt------gacataatttgcatctagcgaattttatgcagttaaaatctattccaa-----gggcactcc----taggcagaat------------------------------------------------------------

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|19057928|gb|BM736595.1|BM736595
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTCGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|60399168|gb|DN231982.1|DN231982
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|87152813|gb|DY397602.1|DY397602
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTCGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|6826953|gb|AW330596.1|AW330596
EST:     TTGGTGATAAACTCTTGAAGCCGNATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|19855109|gb|BQ060161.1|BQ060161
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTCGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|211336615|gb|FL398412.1|FL398412
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|60341783|gb|DN208756.1|DN208756
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTCGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|5525216|gb|AI861214.1|AI861214
EST:     TGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGNCAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|60394820|gb|DN227689.1|DN227689
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTCGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|60347289|gb|DN214262.1|DN214262
EST:     GGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: GGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|60344579|gb|DN211552.1|DN211552
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|60348720|gb|DN215693.1|DN215693
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|71419053|gb|DR804631.1|DR804631
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|6827326|gb|AW330969.1|AW330969
EST:     CGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGNCAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: CGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
EST: gi|211247655|gb|FL406574.1|FL406574
EST:     TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAG                         GAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA
genomic: TTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatg ... ttacaatcagGAGGAGGTGGTCGACAGCTCCCTTGAATTCCTCATCCTTGCTAGCGACGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACATGGAGAGTGGGTGGCGTTCTCGCTGTCTCTCGAGCATTTGGTGATAAACTCTTGAAGCCGTATGTTGTTGCTGACCCTGAAATCAAGgtttgtcatgcatttttgtttttactatggattgcctggatattttttccaaacatatcatggtttgaggaaatatggtgcgtttgtaataaatgcctaaaaacggggatcccatcataagcaatgtcatacatcactcccaacccccctgtagccatctgaaaacggcttttgctattacaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC