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'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGATGATGTATGGCGATATGTTGGAAAACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAGgtttgttcctatcatcaaacaaatgtatgataatatttttgcaaaaagatactgcaatcgctttacgactaaggaatgcgctatgttctatccggtggtattgtcag

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 39
GGGATGATGTATGGCGATATGTTGGAAAACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAGgtttgttcctatcatcaaacaaatgtatgataatatttttgcaaaaagatactgcaatcgctt--tacga-ctaaggaatgcgctat-gttctatccggtggtattgt--cag
| |||||||||||| |||||||||||||||| || ||||| |||||||||||||| |||||||| |||||||||||||||  |  |||| | |  || |     |       ||||||   |||  |||   |||| | |  ||  | || |||  ||    ||  | || |  ||||||||| |   ||
GAGATGATGTATGGAGATATGTTGGAAAACTTTCGGATGCTCAAAGAAGCATGCTTGATGATAGATTTAAATGGAAGgttattgtctatgaccctaccagacctt-------tttttgtttaaaattacaa-aatcacctggtataatctgaggtgtgtatgattatgctgtttggtggtattatattag
















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|28909669|gb|CB331043.1|CB331043
EST:     AACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAG                         GCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
genomic: AACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAGgtttgttcct ... gtattgtcagGCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
EST: gi|4730484|gb|AI649650.1|AI649650
EST:     AACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAG                         GCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
genomic: AACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAGgtttgttcct ... gtattgtcagGCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
EST: gi|19822659|gb|BQ048683.1|BQ048683
EST:     AACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAG                         GCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
genomic: AACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAGgtttgttcct ... gtattgtcagGCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
EST: gi|18649578|gb|BM498397.1|BM498397
EST:     TAGGTTTAAATGGAAG                         GCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
genomic: TAGGTTTAAATGGAAGgtttgttcct ... gtattgtcagGCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
EST: gi|18450764|gb|BM429042.1|BM429042
EST:     TAGGTTTAAATGGAAG                         GCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
genomic: TAGGTTTAAATGGAAGgtttgttcct ... gtattgtcagGCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
EST: gi|18648832|gb|BM497651.1|BM497651
EST:     AACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAG                         GCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA
genomic: AACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAGgtttgttcct ... gtattgtcagGCAAGAGAAATGGATAAAAGGAGAGAAGGAAGGCCTGGTGACGCTCGAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGATGATGTATGGCGATATGTTGGAAAACTCTCAGATGCCCAAAGAAGCATGCTCGATGATAGGTTTAAATGGAAGgtttgttcctatcatcaaacaaatgtatgataatatttttgcaaaaagatactgcaatcgctttacgactaaggaatgcgctatgttctatccggtggtattgtcag

- - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG