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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattgttaacactatcagctacattccacagctatatgacacacttaagcactatattctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag

Basic information

species Zea mays
transcript GRMZM2G175419_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G35990.1 (Glycine max), 5'ss of exon 5
CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattgttaacactatcagctacattccacagctatatgacacacttaagcactatatt---ctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag---
|  |||| ||  | ||||| || ||||||||||| || ||||||||||| ||||| || ||||||||||  || ||  |||||||||| |  ||    ||||      || |     |  ||      | | ||||   |      | ||||||     ||||   ||  | |  ||  ||    ||||| | | |   | ||   || | |||   | ||    
CCCGAGATTGCAAAGCTGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTCGAGgtaggccatgatgtagtttccaaacttctgctacagtgttgatttgctcttaagatggttattgatctcttatggatt-ttatgagctttaaatcattgatttcaatgttgaattgttctaacag

upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G33270.3 (Glycine max), 5'ss of exon 4
CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgt-gtttattgttaacactatcagctac-attccacagctatatgacac--acttaagcactatattctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag---
|  |||| ||  | || || || ||||||||||| || ||||||||||| ||||| || ||||||||||  || ||  |||||||||| |  ||  | |||| |   ||  |  |   |   | || | |   |      || ||      || |    | |    |||| ||  | | ||   |   ||  || |  || ||   ||  | |||   | ||    
CCCGAGATTGCAAAGCCGGGGATTGGAAGAACAAGTGTTACCGTTGTGGGGAAAGAGGTCATATAGAAAAGAACTGTAAGAACAGTCCCAAAAAGTTGAGgtaggccataatctaatttccaaacttctacctcgtgttgatttgctcttaacatggttattgctctctaatgggttttat--gagctttaaatcattgatgtcaatt--tgaattgttctaacag

upper sequence: GRMZM2G175419_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 5'ss of exon 3
CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtt----tattgttaacactatcagctacattccacagctata----tgacacacttaagcactatattctagtgtatatcattgaa-tgctttcat-taaagaagttgcttgctaaatatgtttag------------
|  |||| ||  | ||||| ||||||||||| || || || || ||||| ||||| || ||||| |||||||| |||||||||||||| ||||| ||||||| ||    ||| || |  ||   |    ||||| | |  ||       |||||   ||   ||   |||  |  |||  | |||   | || |    |  ||||   ||| | ||| || |   |||             
CTCGAGATTGCAAAGCTGGAGACTGGAAGAATAAGTGTTATCGGTGTGGAGAAAGAGGTCATATTGAAAGAAACTGCCAGAACAGTCCCAGGAAGCTCAGgtattctcatatggtgattacatgccaaaacatttctctcctgctgccttgacatttttttccatattatatttttgttaagcatgatactgttactgtgcaaagtttttgttagcttaaaactattatgttatattgcag

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|101391570|gb|EB817721.1|EB817721
EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
EST: gi|31360494|gb|CD444851.1|CD444851
EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
EST: gi|113808432|gb|DW929109.1|DW929109
EST:     GAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
EST: gi|31360368|gb|CD444725.1|CD444725
EST:     AATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: AATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
EST: gi|61118470|gb|DN559431.1|DN559431
EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
EST: gi|67025176|gb|CO453925.1|CO453925
EST:     GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAG                         GCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG
genomic: GAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattg ... atatgtttagGCGTGAGAGAAGCTATTCACGGTCTCCATCCCCACGCCGAGGACGGGGCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAGACTGTCAGGCTGGTGACTGGAAGAACAAATGCTACCGTTGTGGCGAAAGGGGCCATATAGAAAGAAATTGCCAGAACAGTCCAAGGAACCTCAGgtgtttattgttaacactatcagctacattccacagctatatgacacacttaagcactatattctagtgtatatcattgaatgctttcattaaagaagttgcttgctaaatatgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA