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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttttaatcataaaattttcagttacttttcaccatgtgaaatgttcatgcttaatacttaggcatatctataaggtagctttcatcctttgatatcattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG

Basic information

species Zea mays
transcript GRMZM2G375504_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375504_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g38150.2 (Oryza sativa), 3'ss of exon 9
gtagtttttaatcataaaattttcagttacttttcaccatgtgaaatgttcatgcttaatacttaggcatatctataaggtagctttcatcctttgatatcattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG
                 | |||    |  |  | |||  |||   ||  |  | |  ||||| ||    ||  | |||| || ||   ||  | ||  ||  |||| |||||||| ||||| ||| |||||||||| |||||||||||||| ||||||||||||||||| || ||||| |||||  |||| ||||||
---------------gtattttgttctggcaatgcactgtgttccattcttttccagaatacata----tacttctaag-taacta--attttgtgtcattgttgt-tagATTGCATCTTTGGCAATTCGAAGTGGTAATGGTCTTCTCCTAAAAGGTGGAAAAGAAGCTATCAGATCAAACACGATATTGCATAAG

upper sequence: GRMZM2G375504_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 10
gtagtttttaatcataaaattttcagttacttttcaccatgtgaaatgttcatgcttaatacttaggcatatctataaggtagctttcatcctttga--tatcatt-gtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG
  || | |||  |||  ||||   ||||  || |  |    | || ||||  ||||   | | |   |||   | ||||  | | | |||  || |   | | ||| |   |||| || || |||||| | |||||||| ||||| |||||| |||||||||||||||| |||| | |||| ||  || | || || |||
-gagctatta--catggaattaa-agttgtttgtttc----ttaattgtt-gtgctattttccttatcat---tttaagtcaacat-catttttgggggtgtgatttgaacagATAGCTTCATTAGCAATCCGAAGTGGGAATGGACTTCTCTTGAAAGGTGGAAAAGAGGCCAAGCGATCTAATGCAATCTTGCACAAG
















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|213179639|gb|FM187655.1|FM187655
EST:     TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAG                         ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
genomic: TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAGgtagttttta ... cattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
EST: gi|211356647|gb|FL094993.1|FL094993
EST:     TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAG                         ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
genomic: TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAGgtagttttta ... cattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
EST: gi|60348148|gb|DN215121.1|DN215121
EST:     TGAGT-CAGGCCTGATGCCTTAGTCCAG                         ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
genomic: TGAGTCCAGGCCTGATGCCTTAGTCCAGgtagttttta ... cattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
EST: gi|32934077|gb|CF038889.1|CF038889
EST:     TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAG                         ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
genomic: TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAGgtagttttta ... cattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
EST: gi|32934404|gb|CF039216.1|CF039216
EST:     GATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAG                         ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
genomic: GATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAGgtagttttta ... cattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
EST: gi|67032674|gb|CO461423.1|CO461423
EST:     TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAG                         ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
genomic: TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAGgtagttttta ... cattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
EST: gi|6564207|gb|AW231829.1|AW231829
EST:     TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAG                         ATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA
genomic: TGGGTGTGCTGTTGATTGTTTTTGAGTCCAGGCCTGATGCCTTAGTCCAGgtagttttta ... cattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatacttaggcatatctataaggtagctttcatcctttgatatcattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG
             atatctataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtttttaatcataaaattttcagttacttttcaccatgtgaaatgttcatgcttaatacttaggcatatctataaggtagctttcatcctttgatatcattgtgtagATTGCGTCTTTAGCAGTTCGAAGTGGCAATGGTCTTCTCCTGAAAGGTGGAAAAGAAGCCATGAGATCGAACACAGTATTACATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC