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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagggcattcttcagaaatttgctgatcccttttggtattatttttaaaaaaatgaagttgcacaagcatactcaacttttcag

Basic information

species Zea mays
transcript GRMZM5G846548_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846548_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g11500.1 (Oryza sativa), 5'ss of exon 9
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagggcattcttcagaaatttgctgatcccttttggtattat-ttttaaaaaaatgaagttgcacaagcatactcaacttttcag
|||||||||||||||||||||||||||||||  |||| ||||||||||||||||| ||||||||||||||||| |||||||||||||  | |     ||||   | ||        ||  || | |  ||  |||    ||| || || |||| ||||||||||||||||||||
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCGTTAACCCAGCATTTTGCACTTGCCAATAATGCAGCTGATATATCTGCAAAGgtaactttgcattatcttgtaacatcctaaatgccaattagatggtaaatttctctaaactgtagctgcagaagcatactcaacttttcag

upper sequence: GRMZM5G846548_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G13010.1 (Glycine max), 5'ss of exon 5
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgt--aagctagggcattcttcagaaatttgctgatcccttttgg--tattatttttaaaaaaatg---aagttgcacaagcatactcaacttttcag--------------------------------
|||||||||| |||||||| |||||||||||  | || ||||||||||| |||    ||||||| || ||||| |||||||||||  ||| ||      |  | |    || | | ||    |  |   ||   | |||||  |  ||   |  ||    |    ||   |  |||| |                                 
CTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAGgttcaagttacatttattctaactgtttagatcattatctgagagttaaagtctttaatgagttgtgcattttttttatatgtatgtatattttgacttattaacatatatatatatatatatatatag

upper sequence: GRMZM5G846548_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G07190.2 (Glycine max), 5'ss of exon 9
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgta--agctagggcattcttcagaaatttgctgatcccttttggtattatttttaaaaaaatgaagttgcacaagcatactcaacttttcag-------------
|||||||||| ||||| || |||||||||||  | || ||||||||||| |||    ||||||| || ||||| |||||||||||   || ||  |  |  | ||    || | | ||   ||  |   | || | ||     ||  |||||  ||   ||| |  |||| | |              
CTGGTGTTGCAAGTGGTGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAGgttctagttacagt-tattccaactgttagatcattatttgagagttaatgtcta----tattcagttgggcatatatatttgacttattaatgtatatctatag

upper sequence: GRMZM5G846548_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G13770.2 (Arabidopsis thaliana), 5'ss of exon 8
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagggcattcttcag---aaatttgctgatcccttttggtattatttttaaaaaaatgaagttgcacaagcatactcaacttttcag--
|||||||||| ||||||||||| |||||||| ||||| ||||| ||||| |||  | | |||||||| ||||| ||||| ||||||  ||       |  |||     |||    |     || |   | | |  ||| |  || |     |   |    ||  | | || || |   
CTGGTGTTGCAAGTGGAGCAACCAGAGCAGCTCTAACACAGCACTTTGCTCTTCAAGACAATGCAGCGGATATATCTGCTAAGgtactctttacttcttgtcactgtgaatgatatagaaactataaatgtgaactttgagtaatt----ctttgcttctat-tttatctattgaaag

upper sequence: GRMZM5G846548_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv01s0011g00500.t01 (Vitis vinifera), 5'ss of exon 9
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgta--agctagggcattcttcagaaatttgctgatcccttttggtattatttttaaaaaaatgaagttg--cacaagcatactcaacttttcag---
|||||||||| ||||||||||||||||| ||| | || || |||||||| |||  ||||||||| || ||||| ||||| |||||   ||     |||||||   |   |     ||  |  |      ||||  ||||  || |    |    ||  | | |  |  |   ||      
CTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAGgtgtgagtataagcattct---gggctggatggaaactatacaaacttatgattaagtaactagtttcaaccatcaacttgttttatactttgacag

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|18654521|gb|BM499326.1|BM499326
EST:     TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG                         GAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
genomic: TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagg ... aacttttcagGAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
EST: gi|18654522|gb|BM499327.1|BM499327
EST:     TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG                         GAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
genomic: TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagg ... aacttttcagGAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
EST: gi|18649151|gb|BM497970.1|BM497970
EST:     TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG                         GAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
genomic: TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagg ... aacttttcagGAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
EST: gi|88755251|gb|DY539392.1|DY539392
EST:     TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCCAAG                         GAAGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGGTGGGG
genomic: TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagg ... aacttttcagGAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGG
EST: gi|18648891|gb|BM497710.1|BM497710
EST:     TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG                         GAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
genomic: TAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagg ... aacttttcagGAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
EST: gi|211102153|gb|FL034739.1|FL034739
EST:     ATTTCTGCAAAG                         GAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG
genomic: ATTTCTGCAAAGgtaagctagg ... aacttttcagGAGGGCAGTCAGGAAACACTTGCTACAATGTTAGGGATGGGGTTGGGGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAGgtaagctagggcattcttcagaaatttgctgatcccttttggtattatttttaaaaaaatgaagttgcacaagcatactcaacttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG