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

gcatgttcattctgccattcattctttgtctttttcttaagctaacgaccctggagtttagtattcacaatggattttttgttttttgattaccattttccttgtgaatctacgtttgacatgtgcattgatatcagaaacctatttttttgtctgtagACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG

Basic information

species Zea mays
transcript GRMZM2G044527_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044527_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g07000.1 (Oryza sativa), 3'ss of exon 3
-------------gcatgttcattc--tgccattcattctttgtctttttcttaagctaacgaccctggagtttagtattcacaatggattttttgttttttgattaccattttccttgtgaatctacgtttgacatgtgcattgatatcagaaacctatttttttgtctgtagACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG
              ||  | |||||  | |  |   ||  | ||| || ||||   || | ||   || | ||| ||| |  ||   ||  | |  | || ||  ||  | |||  |  |||||  |  |||  ||| |  | |  |   | | |||| |  |||||  |||||||||||||||||||||| ||||| ||||||||||||||   ||||||||
gtttatttatctcacacttccattcatttctttctgtttctggtccttgtcttgttctgatgatattg-attttcgtagtacca---gaaatataatgttgtgtcta--agttt--tgatgaattca--tttagcatcttgaattttcatatacacct-tacttttgcttgtagACTGCAAATGAGGAATCTAAAGCGGTTACAAAAGCAAGGGACATGAAAG
















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|211326768|gb|FL451144.1|FL451144
EST:     CAATTGAGAGTATAATTGCAAAGCTGTCAAATCTATTGAATAAGCTCCAG                         ACCGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG
genomic: CAATTGAGAGTATAATTGCAAAGCTGTCAAATCTATTGAATAAGCTCCAGgcatgttcat ... ttgtctgtagACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG
EST: gi|78119539|gb|DV537923.1|DV537923
EST:     CTGTCAAATCTATTGAATAAGCTCCAG                         ACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG
genomic: CTGTCAAATCTATTGAATAAGCTCCAGgcatgttcat ... ttgtctgtagACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG
EST: gi|148932260|gb|EC875796.2|EC875796
EST:     CAATTGAGAGTATAATTGCAAAGCTGTCAAATCTATTGAATAAGCTCCAG                         ACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG
genomic: CAATTGAGAGTATAATTGCAAAGCTGTCAAATCTATTGAATAAGCTCCAGgcatgttcat ... ttgtctgtagACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatctacgtttgacatgtgcattgatatcagaaacctatttttttgtctgtagACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG
                     cattgat  putative branch site (score: 4)
                                    cctatttttttgtct  putative PPT
                                 aaacctattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgttcattctgccattcattctttgtctttttcttaagctaacgaccctggagtttagtattcacaatggattttttgttttttgattaccattttccttgtgaatctacgtttgacatgtgcattgatatcagaaacctatttttttgtctgtagACTGCAAATGAGGAATCCAAAGCAGTTACAAAAGCAAGTTCCATGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG