Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcatcatcagtaacatttgaactctaaatagaacttcagtttaaatgttcatctgatttattgactgttttctatcttttcag

Basic information

species Zea mays
transcript GRMZM5G868757_T07
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 2
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcatcatcagtaacatt-tgaactctaaatagaacttca--gtttaaatgttcatctgatttattgactgttttctatcttttcag-------------------------------------
 ||||| ||||| ||||||||||| || || |||||||||||||||||||| |||||||||||||| ||||||||||| || ||||||||||||||||| |||| |  ||    || | ||||     |    |||||| | |||    | | | |  | |  | | | |     |  | |  || || |  |                                     
GTACCATAAGGCTTGCCAAGAATTCGCTGAATTCTATAAGAATGCTCTTCTTTATCTGGCCTACACTACTGTGGAGTCGCTCTCTGAGTCATTCAAGCTGgtat-taacaatgccaattacataacagaaaaaaaatagcatttcctcctctcattagttagtttaataacaacatactgtgcatattgtttgtattgataatttaccctttgacactgtcatgtgtcag

upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 2
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcatcatcagtaa--catttgaactctaaatagaacttcagtttaaatgttcatctgatttattgactgttttctatcttttcag---------------------
 ||||| |||||  ||||||||||||| |||||||| |||||||| ||||| |||||||| ||||| ||||| ||||| || |||||||| ||||| || |||||||  ||  | |  ||  || ||  |    ||| |    ||   |       ||  | | ||    |  ||    ||||| ||| |                       
GTACCATAAGGCTCGCCAAGAATTTGCTGAGTTCTACAAGAATGCCCTTCTGTATCTGGCTTACACTACTGTAGAGTCACTCTCTGAGTCTTTCAAACTGgtatgttctattgttaacaatgcaattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcag

upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcatcatcagtaacatttgaactctaaatagaacttcagtttaaatgttcatctgatttattgactgttttctatcttttcag--------------
 |  || ||| |  | ||||||||||| |||||||| || | ||| ||||||||| |||| |||||| | ||||| ||||| ||||| ||||||||||| ||||||  |||||  | |    ||  |  | |   | ||   |    ||   ||||  ||| |  |  || || ||| ||     || |               
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgt--catcag-aattgtcttaaatgtttttgttgattgttgccttttttgtt-gtctcaaatcatggctatttacttgtactttactctgattatggtgt

upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G34310.1 (Glycine max), 5'ss of exon 2
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttc----atcatcagtaacatttgaact--ctaaatagaacttcagtttaaatgttcatc-tgatttattgactgttttctatcttttcag---
 |  || ||| | |||||||||||||| |||||||| || | ||| ||||||||| |||| |||||| | ||||| ||||| || || ||||||||||| ||||||       ||  ||   ||  |||    |   |   |    ||| | | |      ||||    ||||| | ||  | | || |  ||   |   
GTTTCATAAGACATGCCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattggttccttctttattgtctcaaatcatggctatttacttacactgtactctggttatggcat

upper sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtt--tcat---catcagtaacatttgaactctaaatagaacttcagt---ttaaatgttcatctgatttattgactgttttctatcttttcag--
 ||  | ||  |  | |||||||| ||||| |||||||| | ||||||||| |||||||| |||||| | ||||||||||| |||||  |||| ||||| |||||||  ||||   | | | | |  |   ||   | ||   |  |  | |   | | ||  |  | | | || || |   | || |  | | |||   
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttactcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactttcacttgttaaggctgttttgacatctcatgt

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|149078129|gb|EE166878.2|EE166878
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
EST: gi|148986083|gb|EE029890.2|EE029890
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCTCTA
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCTCTA
EST: gi|148965470|gb|EE016279.2|EE016279
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCTCTAG
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCTCTAG
EST: gi|194716906|gb|FK934065.1|FK934065
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
EST: gi|148930110|gb|EC872431.2|EC872431
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
EST: gi|148948407|gb|EC893924.2|EC893924
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
EST: gi|211082970|gb|FL307146.1|FL307146
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
EST: gi|148982851|gb|EE028701.2|EE028701
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCT
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCT
EST: gi|6020572|gb|AW065605.1|AW065605
EST:     TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTA                         GACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC
genomic: TCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttca ... atcttttcagGACTTGGCTTTTGATCTATCTCTAGCAGCCTTGCTGGGTGATAACATTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcatcatcagtaacatttgaactctaaatagaacttcagtttaaatgttcatctgatttattgactgttttctatcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT