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

AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatatctgaaattcttgtgtacttctttgggcgagatggacaggtctggtgcagtggtgagaagccttcatactgagccaaaggtcctgtgtttg...

Basic information

species Zea mays
transcript GRMZM2G420865_T02
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 5'ss of exon 15
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatatctgaaattct-tgtgtacttctttgg-gcgagatggacaggt-ctggtgcagtggtgagaagccttcatactgagccaaaggtcctgtgtttg
||||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||| | ||| |||||||||||||||   || |||||||||||     || ||||| | | | || |||||||  || | || | ||  | |   ||||      ||   |  ||| | || |||    | |   ||  ||
AGAAAATATGATAGCTCATAAGGATGAGATATACTCAAGACCAAAGAGAACCTGGTTTGCTACTGAGAAGGAAAAGAAACTTTTGGCAAAGGCTGCTAAAgtaagttcgccttaaattgtatatatatttctttgatgccaaattgccaattacatatgcaaattctag---ctctcaaattgtgcctgctgcctgctgcatg

upper sequence: GRMZM2G420865_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 5'ss of exon 15
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatatctgaaattcttgtgtacttctttgggcgagatggacaggtctggtgcagtggtgagaagccttcatac-tgagccaaaggtcctgtgtttg
 ||||| ||||| || ||||||||||| || |||||||| || || |||||||||||||| || |||| |||||||||   | |||||   || || || ||||    || |   |   |||| |  || ||||       | |  ||      |  | || ||   |   ||  |   ||||       | |  | ||  
TGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAAAGgtaatttcatattgcaccattgt-tgtttatttgtattcatttgtaagtctatatataatgttgtatatgttttgtctgtgagttggcatttccatattct
















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|78090028|gb|DV518402.1|DV518402
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|78027541|gb|DV495928.1|DV495928
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|37373944|gb|CF623297.1|CF623297
EST:     TGAAAGGGAGAAGAAACTTTGGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: TGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|211352888|gb|FL146172.1|FL146172
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAAGAA
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAA-GAA
EST: gi|211352883|gb|FL146167.1|FL146167
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGT
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGT
EST: gi|60396007|gb|DN228877.1|DN228877
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|4887454|gb|AI677553.1|AI677553
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTCCTAA
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAA
EST: gi|37398106|gb|CF636362.1|CF636362
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|40337352|gb|CK371422.1|CK371422
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|31349040|gb|CD433397.1|CD433397
EST:     CCTGGCTTGCTACTGAAAGGGAGAATAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGA
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGA
EST: gi|211352887|gb|FL146171.1|FL146171
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCA
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCA
EST: gi|211352885|gb|FL146169.1|FL146169
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|4887453|gb|AI677552.1|AI677552
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGAT
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGAT
EST: gi|33100275|gb|CF060235.1|CF060235
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGT
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGT
EST: gi|78090029|gb|DV518403.1|DV518403
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGG
EST: gi|60344195|gb|DN211168.1|DN211168
EST:     TTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: TTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
EST: gi|60341880|gb|DN208853.1|DN208853
EST:     CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAA                         GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG
genomic: CCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatat ... tttcataaagGAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTAAAgtaagcatatctgaaattcttgtgtacttctttgggcgagatggacaggtctggtgcagtggtgagaagccttcatactgagccaaaggtcctgtgtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA