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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACGGATGACCTAAGACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaagactggtattgtttggcatgtcataatatattagttgtctcaactcttcaaatttccatacag

Basic information

species Zea mays
transcript GRMZM2G030902_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 11
GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACGGATGACCTAAGACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaagactggt--attgtttggcatgtcataatatattagttgtctcaac-tcttcaaatttccatacag
 |||||||||||||| || ||||||||||| ||||||||||| |||||||| ||||||||||||| |||||| ||||| || ||||| ||||| ||||||||   | |||||||     ||||||||  |     || ||| ||| |   |||||| | ||| ||||    |  ||
AAAGATATTTGTTGGCAGGCTTCCACAAGAGGCAAACACGGAGGACCTAAGGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaagactttctcattgtttgtaac--tgtactatgttaat---ctcaaccttttctaattgtattgaag
















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|22490941|gb|BU050864.1|BU050864
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCNCCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|32912299|gb|CF017111.1|CF017111
EST:     ATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: ATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|87151821|gb|DY396610.1|DY396610
EST:     GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|19436499|gb|BM952909.1|BM952909
EST:     TTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAG                         GACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: TTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaa ... ttccatacagGACCCCAAAAGAAGTGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACGGATGACCTAAGACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaagactggtattgtttggcatgtcataatatattagttgtctcaactcttcaaatttccatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT