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

AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactctacactcagtgctttcttgaggaccaataaaataaatactcactccgttccgatttataatttgtttgactttttttattctaagt...

Basic information

species Zea mays
transcript GRMZM2G161168_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161168_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g70390.1 (Oryza sativa), 5'ss of exon 12
AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactctacactcagtgctttcttgaggaccaataaaataaatactcactccgttccgatttataatttgtttgactttttttattctaa-gt----
||| || |||||| |||| ||||||||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||||||||||||||| ||||| |||||||  ||   |  |    || |||  || || |  |  | |  | | |||    |         || | || | | ||  ||| |  ||||| | ||    
AACATATCAAAACCTAATAACTCAATCAATGTATGACAAACAGCTAGATAGTGGGAAAGGCACACTTCTCCATCTCTGTGATGATGTGATTCAGCAGGAAgtaggtctccatattgta----gtacttgattcagaataagcatatcagagacttgtgctcacaattattttcatctttgtgg-tttctgaattctgatgtccag

upper sequence: GRMZM2G161168_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA16G05180.1 (Glycine max), 5'ss of exon 12
AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactc--tacactcagtg-ctttcttgaggaccaataaaataaatactcactccgttccgatttat-aatttgtttgactttttttattctaagt
    |||||||| || || || || |||||||||||||||||||| || ||||| || || || || || ||  | ||||||||||| ||||||||||| ||| || |   ||   | || || ||| |||| ||      |   |||  ||||    |    | |    ||| | ||| | |||    || ||||        
TCAGTACCAAAATTTGATTACGCAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACGCTTCTTCATTTGTGTGATGATGTCATTCAACAGGAAgtaagtgccagcttgatgcattctgtgtctttgttttttgtcttcaaatcaaatcagtatattgataatttttgttaatgtttttagaattgtttagaaa----

upper sequence: GRMZM2G161168_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA16G26360.1 (Glycine max), 5'ss of exon 12
AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactctacactca-gtgctttcttgaggaccaataaaataaatactcactccgttccgatttataatttgtt-tgactttttttattctaagt-----
    |||||||| || || ||    |||||||||||||||||||| || ||||| || || ||||| |||||  | ||||||||||| ||||||||||| ||| ||  ||   |||  || |  ||| || |       || || |||   |  | | |   |||| ||  || | | ||    | |||| |||   ||  |     
CCAATACCAAAATTTGATTACAAGGTCAATGTATGACAAACAACTGGACAGTGGAAAGGGTACACTTCTCCATTTATGTGATGATGTCATTCAACAGGAAgtaagt--actagctaggctgatatgccttgt-----gtcattataattttttttaaattatttccaatgaattagtagtgacaatttttgttaacttattttgcca

upper sequence: GRMZM2G161168_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G07370.1 (Glycine max), 5'ss of exon 12
AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactctacactcagtgctttcttgaggaccaataaaataaatactcactccgttccgatttataatttgtt-tgactttttttattctaagt----
    |||||||| || || || |  |||||||||||||||||||| || ||||| || || ||||| |||||  | ||||||||||| ||||||||||| ||| || |   |   |      ||||||| |       || |    |   |  | | |   |||| ||  || | | ||  | | || | |||   |   |    
CCAATACCAAAATTTGATTACACGGTCAATGTATGACAAACAACTGGACAGTGGAAAGGGTACACTTCTCCATTTATGTGATGATGTCATTCAACAGGAAgtaagtgctagcatgat-----gtgctttgtgtcattacatttgttttgttttttaattttttccaataaatcaatagtgataatttctgttaacttgttttgcc

upper sequence: GRMZM2G161168_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA19G27800.1 (Glycine max), 5'ss of exon 12
AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactc--tacactcagtgctttcttgaggacc--aataaaataaatactcactccgttccgatttataatttgtttgactttttttattctaagt---------------------------------------------------------------------------------------
    |||||||| || || || || |||||||||||||||||||| || ||||| || || ||||| || ||  | ||||||||||| ||||||||||| ||| || |   ||   | || || ||| ||| ||  |      ||| |||| | ||         ||    || ||  ||| |   | | |||  |   || |                                                                                        
TCAGTACCAAAATTTGATTACACAGTCAATGTATGACAAACAACTTGACAGTGGAAAGGGTACACTTCTTCATTTGTGTGATGATGTCATTCAACAGGAAgtaagtgccagcttgatgcattctgtgtttttttttgtcttcaaatcaaatcagtatattgataatttttgttaatg-tttttagaattgtttagaaagtaggatagggctggctgttctaattgtacctgaaactggccagcttatttctgcacaaccctcaattctttcttgctttggtttgactctag

upper sequence: GRMZM2G161168_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv14s0068g00980.t01 (Vitis vinifera), 5'ss of exon 12
AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactctacactcagtgctttcttgaggaccaataaaataaatactcactccgttccgatt-tataatttgtttgactttttttattctaagt
    ||||| ||||||||||| |  || ||||| ||||||||||| |||||||| |  || || || || ||| | |||||||||||||||||||| || ||| ||      |||| |   |    |||    | |   | |    | || | | |||  | |||  || ||| |  |||   | |  |   |    ||  
TGAGTACCAGAACTTAATCACACGGTCCATGTACGACAAACAACTGGATAGTGGAAGGGGAACTCTGCTTCACTTGTGTGATGATGTGATTCAACAAGAAgtaagtat-tgatctagaagaacattttttaatatgttaagtctttttaaaattgactatgctccatttgtatcacatgtagtattagtgaaagataaaaa

upper sequence: GRMZM2G161168_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 5'ss of exon 12
AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactctacactcagtgctttcttgaggaccaataaaataaatactcactccgttccgatttataatttgtttgactttttttattctaagt----
  | || || ||||||||||| ||||| |||||||| || || || |||||||| || || || || || ||| | |||||||| ||||||||||| || ||| || |  |   || |    |   |||  |     ||||||   |      ||       ||    | ||  ||| |||   |      || |  |      
TGCATATCAGAACTTAATCACACAATCCATGTATGATAAGCAGCTGGATAGTGGAAAGGGTACTCTTCTTCACTTGTGTGATGACGTGATTCAACAAGAAgtaagttc-taaaataga---ggaattttaattctatccaatattttggtctttcttgatagtcaatatgatttttttttttggtgaaaccatacagaaaattt

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|118406769|gb|EH038217.1|EH038217
EST:     GTGGGAAAGGCACACTTCTCCACCTCTGTGATGATGTGATTCAACAGGAG                         GTCAAGGAGGTCATAATTGCCTACTACATTTTGATGGAGAATGGAAAGGCT
genomic: GTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccac ... caacgttcagGTCAAGGAGGTCATAATTGCCTACTACATTTTGATGGAGAATGGAAAGGCT
EST: gi|71426967|gb|DR808017.1|DR808017
EST:     GTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAG                         GTCAAGGAGGTCATAATTGCCTACTACATTTTGATGGAGAATGGAAAGGCT
genomic: GTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccac ... caacgttcagGTCAAGGAGGTCATAATTGCCTACTACATTTTGATGGAGAATGGAAAGGCT
EST: gi|40334664|gb|CK368734.1|CK368734
EST:     GTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAG                         GTCAAGGAGGTCATAATTGCCTACTACATTTTGATGGAGAATGGAAAGGCT
genomic: GTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccac ... caacgttcagGTCAAGGAGGTCATAATTGCCTACTACATTTTGATGGAGAATGGAAAGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCTACCAAAACTTAATCACTCAATCAATGTATGACAAACAACTAGATAGTGGGAAAGGCACACTCCTCCACCTCTGTGATGATGTGATTCAACAGGAGgtaggtccacactctacactcagtgctttcttgaggaccaataaaataaatactcactccgttccgatttataatttgtttgactttttttattctaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataaa