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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctctaatacaccactgtgctgtgcatccatacatagtaccatgccacgcatagaaagagggatcatatatatacgcatagtctcgctgacaatgcaaacgtgattatattatatatatgggcgtatgcag

Basic information

species Zea mays
transcript GRMZM2G118063_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118063_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g08820.1 (Oryza sativa), 5'ss of exon 4
ACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctctaatacaccactgtgctgtgcatccatacatagtaccatgccacgcatagaaagagggatcatatatatacgcatagtc-tcgctgacaatgcaaacgtgattatattatatatatgggcgtatgcag
 ||||| || ||||||||||| |||||||||||| ||||||| ||||| || || |||||||| || |||||||| |||||||||||||||||||||||||||||    || || ||       | |  ||  ||| |  || |  ||        |      ||  ||| |   | | |  | |   |  |||| ||   |||                                
GCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAGgcaagtataaaaactcc------ttatagatatatagagtgttctttggttatttaatttgatggcttcagactaaaatgattgggaattactgaaaaataaaatt------------------------------

upper sequence: GRMZM2G118063_T03 (Zea mays), 5'ss of exon 4
lower sequence: EFJ34024 (Selaginella moellendorffii), 5'ss of exon 2
ACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctctaatacaccactgtgctgtgcatccatacatagtaccatgccacgcatagaaagagggatcatatatatacgcatagtctcgctgacaatgcaaacgtgattatattatatatatgggcgtatgcag
 || || || || ||||||||  ||||||||||||||||||| || || ||||| | ||| ||||||||||||||||||||    ||||| ||| | |||| | | |  ||           |||      ||| |     | |  || |     | ||   |  |||| |   | |  |   ||                                                  
TCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAATCGCCGCACGCAGCTCAAGgtaggatagaa-----------gct------ccaaaagcttttctttggcgtttct-gatgtaaagatcttccttgtctgtccag--------------------------------------------------

upper sequence: GRMZM2G118063_T03 (Zea mays), 5'ss of exon 4
lower sequence: EFJ10492 (Selaginella moellendorffii), 5'ss of exon 3
ACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctctaatacaccactgtgctgtgcatccatacatagtaccatgcca-cgcatagaaagagggatcatatatatacgcatagtctcgctgacaatgcaaacgtgattatattatatatatgggcgtatgcag
 || |||||||||||||||||  ||||||| ||||||||||||||  | ||||||| ||| |||||||| |||||||||||     | || ||| | |||| | |     |       |||   |    |||  | | | |     | ||  |||  ||                                                                             
GCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAATCGAAGGACCCAGCTCAAGgtagggggagagttcttgctggttttcttatcgtttctttgccttgttccgtcgcccag-----------------------------------------------------------------------------

upper sequence: GRMZM2G118063_T03 (Zea mays), 5'ss of exon 4
lower sequence: EFJ37532 (Selaginella moellendorffii), 5'ss of exon 2
ACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctctaatacacca---ctgtgctgtg-catccat-acatagtaccatgccacgcatagaaagagggatcatatatatacgcatagtctcgctgacaatgcaaacgtgattatattatatatatgggcgtatgcag
 || || || || ||||||||  ||||||||||||||||||| || || ||||| | ||| ||||||||||||||||||||    ||||| ||| | |||| | | |  ||    | |   || | || || | |   | || ||      | ||  || |    ||                                                                         
TCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAATCGCCGCACGCAGCTCAAGgtaggatagaagctccaaaagcttttctttggcgtttctgacgtaaagatcttccttgcctgtccag-------------------------------------------------------------------------

upper sequence: GRMZM2G118063_T03 (Zea mays), 5'ss of exon 4
lower sequence: EFJ19972 (Selaginella moellendorffii), 5'ss of exon 3
ACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctctaatacaccactgtgctgtgcatccatacatagtaccatgcca-cgcatagaaagagggatcatatatatacgcatagtctcgctgacaatgcaaacgtgattatattatatatatgggcgtatgcag
 || |||||||||||||||||  ||||||| ||||||||||||||  | ||||||| ||| |||||||| |||||||||||     | || ||| | |||| | |     |       |||   |    |||  | | | |     | ||| |||  ||                                                                             
GCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAATCGAAGGACCCAGCTCAAGgtaggaggagagttcttgctggttttcttatcatttctttgccttgttccatcgcccag-----------------------------------------------------------------------------

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|71767000|gb|DR964937.1|DR964937
EST:     AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAG                         AACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
genomic: AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctcta ... gcgtatgcagAACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
EST: gi|78087580|gb|DV515973.1|DV515973
EST:     AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAG                         AACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACCAG
genomic: AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctcta ... gcgtatgcagAACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
EST: gi|148934302|gb|EC878328.2|EC878328
EST:     AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAG                         ACCCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACCAG
genomic: AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctcta ... gcgtatgcagAACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
EST: gi|149100689|gb|EE186778.2|EE186778
EST:     AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAG                         AACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
genomic: AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctcta ... gcgtatgcagAACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
EST: gi|148953688|gb|EC899049.2|EC899049
EST:     AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAG                         AACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
genomic: AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctcta ... gcgtatgcagAACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
EST: gi|149015319|gb|EE045135.2|EE045135
EST:     AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAG                         AACCAGCACGAGCGGCAAGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
genomic: AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctcta ... gcgtatgcagAACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
EST: gi|71299781|gb|DR785898.1|DR785898
EST:     AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAG                         AACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
genomic: AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctcta ... gcgtatgcagAACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
EST: gi|149102070|gb|EE287534.2|EE287534
EST:     AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAG                         AACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG
genomic: AGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctcta ... gcgtatgcagAACCAGCACGAGCGGCAGGAGAACGCGCAGCTGCGCGCAGAGAACGACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctctaatacaccactgtgctgtgcatccatacatagtaccatgccacgcatagaaagagggatcatatatatacgcatagtctcgctgacaatgcaaacgtgattatattatatatatgggcgtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG