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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag

Basic information

species Zea mays
transcript GRMZM2G023798_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 5'ss of exon 8
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgtt-ctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
||||||||||||||||||||||||||| ||||| |||||||| || || ||| ||||| | |||||| | ||| |||| |||||||||||||| |||||||| |   ||  |  || || |  |      |     | || || |  ||   |  || || ||| || |  ||      |  |    | |  |||  || | |                                         
TGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATGGCATGAAAATGCAGgtcaccttttttctttactctaacttccaacaagaaagttggtaactttggcacaagacacctattgaacaagtgtgatttactgtctatt-gat--gccatt-----------------------------------------

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 5'ss of exon 9
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
|   || ||| | |||||||||||||| ||||| |||||  | ||| | ||  || | | ||||| | ||||||||||||||||||||||||| ||||||||              |      | || || |     ||    || | ||        | | ||  || || ||||      || |   || |  || |||        |        |                        
TTGCTGTTGGGTGGAAGATCCAAACTCAGAGGCTTTCAAGTTACATCTTCCTAGAATTTTTGATTTCCTGTGGCTTGCTGAAGATGGCATGAAAATGCAGgt--------------ccaaaaacaatatcatccctattcacgaagtacc--------aaccacaacaacaacaaaaaaaaaaaaaaaaaaaaagggaaaaaaaaaaaagaaaaaaagaaaa---------------------

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0054g01550.t01 (Vitis vinifera), 5'ss of exon 8
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
|   ||||||||||||||||||||||| |||||||| ||  | ||||| ||| || | | |||||| |||||| |||||||||| |||||||| ||||||||    ||   | ||  |  |     |||  ||||  ||       ||  | || |||   |  ||| | |   ||  |       |  ||  | ||    |||||||    |                              
TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgt--ccataaatagtattaggtggtgttttttttttttt-------tttttttttggc--tttttgctgaaaataatttatt--tttagaatttaggttgtttgtttttatat------------------------------

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0054g01090.t01 (Vitis vinifera), 5'ss of exon 9
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
|   ||||||||||||||||||||||| |||||||| ||  | ||||| ||  || | | |||||| |||||| |||||||||| |||||||| ||||||||    ||   | ||  |        | || || || ||  |          | ||   || | | |      | |  |      ||| |  ||||  | |||  |      | |    ||||   |                
TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCCAGAATTTTTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgt--ccataagtagtatta------gtctctttctagtttatc---------tcagagtgccatttccattttatatgt-----tatggagaattgtgatattact-----atttctggtggatgta----------------

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0054g01200.t01 (Vitis vinifera), 5'ss of exon 2
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
|   ||||||||||||||||||||||| |||||||| ||  | ||||||||| || | | | |||| |||||| |||||||||| |||||||| ||||||||   || |      | | | |   || ||  | | |    ||  | |  |||| || |  || || |       | ||  |    |     |                                                  
TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATCCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgtccgtagt-----ctttctagtttatctcggtgtgcc--atttccattttatt-ggaaattattgaattttattatctatctgtttactgcag-------------------------------------------------

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0054g01180.t01 (Vitis vinifera), 5'ss of exon 7
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtg-------attattgcttgttctgtggcccatttccttttact-tagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaa--attg--ttttggggtct-tcaatggagccagctctttccactgtag
|   ||||||||||||||||||||||| |||||||| ||  | ||||| ||| || |   |||||| |||||| |||||||||| |||||||| ||||||||        | |||| ||   | | |     || ||    | |  ||  || |    ||| ||     |  || |   ||| |  | | |   | |    |||| ||  ||||  ||||    ||| ||  |    |    |   | ||||| ||
TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTATTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgtccataaatagtattactctctttctattttatctcagagtgccatatgtagccatttat-agtggcgtgttgtaaaggcagattttgtattttattcc-ttggaaattattgaattttattatctgtctgtcatacataataagttcactgcag

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 5'ss of exon 10
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
|   ||||||||||||||||||||||| |||||||| ||  | ||||| ||| || | | |||||| |||||| |||||||||| |||||||| ||||||||   | |   | ||  |  | | | ||    ||||  |    | | | | |||      | | |  |   |  |     |  |  ||| | |||    | || || ||| |  |  |                         
TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgt--ctgtaagtagtatta-gtctctttctagtttatct---cagcgtgccattt-----ccattttatatgtta---cagagaattgtgatatt----actttttctggtggatgta-------------------------

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0054g01120.t01 (Vitis vinifera), 5'ss of exon 7
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtg-------attattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagcta-ctgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag--------------------------------------------
|   ||||||||||||||||||||||| |||||||| ||  | ||||| ||| || | | |||||| |||||| |||||||||| |||||||| ||||||||        | ||||  |   | | | |   || ||    | |    |  | ||  |||    | |  |  ||    |  |    |        ||     | || | |  |  ||| || ||   |  || ||| | |||  | | ||                                             
TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgtccgtaagtagtattagtctctttctagtttatctcagcgtgccatttccattttatatgttacggagaattgtgatattactttttctg----gtggatgtagccattcatagtggcgtgtt--gtaaaggcagat-tttgtattttattccttggaaattattgaattttattatccatctgtttaccgcag

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0054g01250.t01 (Vitis vinifera), 5'ss of exon 5
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
|   |||||||||||||||||||||||||||||||| ||  | ||||| ||| || | | | |||| |||||| |||||||||| |||||||  ||||||||    ||   | ||  ||  | |  ||||        ||||| |  ||  | |  ||   | |      |       |||  |  ||| | |||    | || || ||| |  |  |                         
TTGCTGCTGGATTGAAGATCCAAACTCGGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACGGCATGAGAATGCAGgt--ccataagtagtattg--gtctctttc--------tagtttatctcaaagt--gccatttccattttatatgttatggagaattgtgatatt----actttttctggtggatgta-------------------------

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0018g00630.t01 (Vitis vinifera), 5'ss of exon 8
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
|   ||||||||||||||||||||||| |||||||| ||  | ||||| ||| || | | | |||| |||||| |||||||||| |||||||| ||||||||   ||           || | |    ||  |||   ||||| |  ||  |  | ||   | |      |        ||  |  ||| | |||    | || || ||| |  |  |                         
TTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACGGCATGAAAATGCAGgtccgtaa----------gtagtcttagtctcttt--ctagttta--tctcagcatgccatttccattttatatgttacggagaattgtgatatt----actttttctggtggatgta-------------------------

upper sequence: GRMZM2G023798_T02 (Zea mays), 5'ss of exon 6
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgc-ttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag
  | |||||||| || || || ||||| || |||||||| || ||| |  |||| ||    |||||| | ||| | ||||||||||||||||||||||||||   | || | |||| || |  |      | ||  ||||||  |  |   ||||  | |  || |||  ||  ||| || | | || ||   |   | |   ||                                       
GTCCTGCTGGATAGAGGACCCTAACTCAGAAGCCTTCAAGCTGCATTTGGCACGGGTTGTCGATTACCTATGGGTGGCTGAAGATGGCATGAAGATGCAGgtatctttttcattgtacttttacttgca-cattcaacttag--agataaatattcagaacttattgcttca-taaatcttggatcaagttt-accagtatgatg---------------------------------------

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|21331674|gb|BQ487055.1|BQ487055
EST:     CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAG                         GGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT
genomic: CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattg ... tccactgtagGGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT
EST: gi|23199794|gb|BU582359.1|BU582359
EST:     CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAG                         GGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT
genomic: CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattg ... tccactgtagGGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT
EST: gi|9733396|gb|BE512253.1|BE512253
EST:     CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAG                         GGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGNTCAAGCCATT
genomic: CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattg ... tccactgtagGGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT
EST: gi|87156285|gb|DY401074.1|DY401074
EST:     CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAG                         GGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT
genomic: CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattg ... tccactgtagGGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT
EST: gi|26560142|gb|CA832377.1|CA832377
EST:     CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAG                         GGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT
genomic: CACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattg ... tccactgtagGGTTATAATGGCAGCCAACTTTGGGATACAGCTTTCACAGTTCAAGCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATGGCATGAAGATGCAGgtgattattgcttgttctgtggcccatttccttttacttagttaacttcctattaggcagctactgcagcagcaaacctggcaacatgtaagattggcaaattgttttggggtcttcaatggagccagctctttccactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG