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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaaaatctgtgattgattaaaaagagtagactacagagcagccttgttataggttcgagtataactgacacgctgaagtaccattag

Basic information

species Zea mays
transcript GRMZM2G095252_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 11
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgt--aagaacaaaatctg--tgattgatta-----aaaagagtagactacagagcagccttgttataggttcgag---tataactgacacgctgaagtaccattag-------------------------------------------------------------------
|||||||||||||||||||||||||||||| ||||| ||| || | || ||||||| ||| || ||||||||||| |  |||||||| ||||||||||||||  |  | ||  ||||   | ||| |||          ||||   ||| | | |     | | | | ||||      | |  |||  ||  || |      ||||                                                                   
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGCAGAAGgtttacaaccatgatctactttattcattgtttttgttcgagtgttctataaacctcatctctcaaaagttctgtttttgtgcctgctactatgtatatgggttagaaatgaccatctcgaatttgttgtcctttctaattgacttgttgtatgtattgcttgaactttttag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G18760.3 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaaaatctgtgattgattaaaaa-gagtagactacagagcagccttgttataggttcgagta-taactgacacgctgaagtaccattag-------------------------------------------------------------
    ||||||||||||||||||||||| || ||||| ||| || | |||||| | || || ||||| ||||||||||  || || || |||||  | || || ||      || ||  || ||   || |  |||   ||  |        |  || | | || | ||  |     |  | |   | |    ||                                                               
----GAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAGTGAgtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcaggttggag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaaaatctgtgattgattaaaaa-gagtagactacagagcagccttgttataggttcgagta-taactgacacgctgaagtaccattag------------------------------------------------------
||| ||||||||||||||||||||||| || ||||| ||| || | |||||| | || || ||||| ||||||||||  || || || |||||  | || || ||      || ||  || ||   || |  |||   ||  |        |  || | | || | ||  |     |  | |   | |    ||                                                        
TGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaag-aacaaaatctgtgattgattaaaaagagtagactacagagcagccttgttataggttcgagtataactgacacgctgaagtaccattag
|||||||||||||||||| |||||||| || ||||| ||  | ||||||||| | || |||||||||||||||||||| || || || |||||  | ||||| |    |||||||    |||  || |||    | |   |  |      |||  |  |  ||| | |||  |  |  | ||             
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaatt--ttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccat-ctctag-----------

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 10
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaa--caaaatctgtg-at-tgattaaaaagagtagac--tacagagcagccttg-------ttataggttcgagtataac-tgacacgctgaagtaccattag----------------------
 ||||||||||||||||| |||||||| || |||||  | ||||| || ||||| ||||| ||||| ||||| || || || || |  |||||||| ||||| | |     |||  | |  || |||||| |  |  |  |   |   ||   |   |        ||| |  || |  | |||| |||     |||  ||    | |                      
CGTTGAGGAAGGTATTGTGGTTGGTGGCGGGTGCACATTGTTGCGTCTAGCAGCAAAAGTTGATGCTATCAAAGACACTCTTGATAGTGATGAGCAAAAGgtgatacatttaaacttatacatatgattatattgtttttatcttttggaaggggtataaaagtgcttacacttttgcttctaacctgatgtcttgatctaatgcttggtttactgggaatgattggcag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 5'ss of exon 7
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaaaatctgtgattgattaaaaagagtagactacagagcagccttgttataggttcgagtataact-gacacgctgaagtaccattag--------------------------
||| |||||||| |||||||||||||||||||| ||| | ||| |  | ||    |||||   ||| ||       ||  |||| ||||| ||||||| ||||||   | | | | || |  |||   |  |  |   ||||    ||  |||  ||     ||| || ||||  ||  | |    |   ||  |                          
TGTGGAGGAAGGCATTGTTGTTGGTGGAGGATGTACCTTGTTGAGATTAGCTAGCAAAGTTAGTGCTATTGTTTCAACCTTGGATAACGACGAGCAGAGGgtaagtg-atattttatgct--attcctacaatcaagttacaatcaaggtttgacatgaagccga-tacaacttaacttgttatgttcagatctgaattgtctgggtgcctacttctgcag

upper sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S276_75V6.1 (Physcomitrella patens), 5'ss of exon 7
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaaaatctgtgattgattaaaaagagtagactacagagcagccttgttat-aggttcgagtataactgacacgctgaagtaccattag----------------------------------------------------------------------------
||| |||||||| || || || ||||||||||||||| | ||| |  | ||     |||| ||||| ||||| ||||| ||||| ||||||||||||||||| || |        ||||| ||||  |   |||| || ||| || || | | || |  ||   | |      | |   | | || |   ||                                                                               
TGTGGAGGAAGGCATCGTCGTGGGTGGAGGATGCACCTTATTGAGATTGGCTAGCCAAGTGGATGCTATCAAAGATACTCTGGACAACGATGAGCAGAAGgtgagta--------gtgatggatttcatgtagta-acgacacagaagaccttttgttggggggggggggggatcagttgattaattctgatctctactgattttgattgtgttattacgttggaaaggtctttaattatatgatgccactgtcaccctgcctctcgacag

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|32837509|gb|CD977187.1|CD977187
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32932965|gb|CF037777.1|CF037777
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|33092673|gb|CF052667.1|CF052667
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32934171|gb|CF038983.1|CF038983
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGACCGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|211520114|gb|FL350150.1|FL350150
EST:     AGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: AGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32931699|gb|CF036511.1|CF036511
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32935108|gb|CF039920.1|CF039920
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32931097|gb|CF035909.1|CF035909
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32836365|gb|CD976043.1|CD976043
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32935122|gb|CF039934.1|CF039934
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32838764|gb|CD978445.1|CD978445
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|32930569|gb|CF035381.1|CF035381
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
EST: gi|33097092|gb|CF057052.1|CF057052
EST:     CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAG                         GTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT
genomic: CAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaa ... gtaccattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaagaacaaaatctgtgattgattaaaaagagtagactacagagcagccttgttataggttcgagtataactgacacgctgaagtaccattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG