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

...ggcttaatgtttacacgatggtagtagaataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG

Basic information

species Zea mays
transcript GRMZM2G138861_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 5
ggcttaatgtttacacgatggtagtagaata-atgaatatgatcatag--cgttgtcagttttcttttaactaacaa-taccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
    |||  || |   | |   | || | || |     || |   |||  | || || | |||  | |||  | ||| |   |        || || ||||||||| || ||||| ||||| || || || |||||||| ||||| |||||||||||||||||||||||| ||||||| |||||||| |||||||||
----taaatttcatttgcttacaatacactatactggcattactttaggacattatctggtttactctaataagcaaatgataaaagacaatctttttctgcagTCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
-ggcttaatgtttacacgatggtagtagaataatgaatatgatcatagc-gttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
     || ||  |  || |   |||  ||  | ||  |    |  |    ||| | |||||| ||||  | |  |||   ||  ||  |    | |   ||||| || || |||||||| || || ||||| ||||| ||||| ||||| |||||||| || ||||| ||| ||||| |||| ||||||||||||
tacaatagtggatttacaactatagatgatcattgtttcctgttgtttttgttttgagtttttttttcccca--aatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 5
ggcttaatgtttacacgatggtagtagaataatgaatatgatc-atagcgttgtcagttt-tcttttaactaaca-ataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
   |||    |     |    | || || ||||   ||  |||  |  |    | | ||| |  | |   | ||| | | | ||  | | | | | | ||||||| ||||| || ||||| || || || || |||||||| || ||||| || ||||| |||||||||||| | || || |||||||| ||||||
--tttatctgtcctttgcctttggttgattaatttgtaatatctgtgacacaattaatttgtaatatctgtgacacaaatcttgactgtcttact-tttgcagTCCTCTGTGCTACATTCACAACCTAAATCTACTGTTGGTACCCCTGCATACATTGCTCCTGAAGTTTTGCTTAAGAAGGAATATGACGGCAAG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
-----ggcttaatgtttacacgatggtagtagaataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
     |   | ||   |  || |  ||| |   | |   |     || | |  ||||     || || |   |||  |||   ||  |||||   || |  |||||| || || |||||||| || || ||||| ||||| ||||| || || |||||||| || ||||| ||| ||||  |||| ||||||||||||
aaatagaggtcatccatgtacaa--gtaatgacacatcaaggtccatta-atagttgatcaattactatatcctacaaatctaatagatttt--gttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 5
-----ggcttaatgtttacacgatggtagtagaataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
        |     |||  |   |  |  ||   ||| |||| |||  || |  |||     ||||| |   ||   |||   ||  |||||   || |  |||||| || || |||||||| || || ||||| ||||| ||||| || || |||||||| || ||||| ||| ||||  |||| ||||||||||||
tttttctttcgtcctttgtattcta-ttttattttaaagaatttga--attgttttgatcaatttctgtatcctgcaaatgtaatagatttt--gttattggcagTCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
ggcttaatgt-ttacacgatggtagtagaataa--tgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
    || ||  ||  || |   |||    || |  ||  | |  |  ||    | | |||||| ||||    |  |||    |  ||  |    |     ||||| || || |||||||| || || ||||| ||||| ||||| ||||| |||||||| || ||||| ||||||||| |||| ||||||||||||
---atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
ggcttaatgtttacacgatggtagtaga-ataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcattt-ttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
  ||||  ||| |  |  |     || |  |  |   ||  |       ||| ||  |||  |||   || | | ||  |   ||   ||  || ||| ||||| ||||||||||||||||| || ||||| |||||||| || ||||| || |||||||| ||  || |  |   | | |||||||||||||||
-tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctca-agtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG

upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------------------------ggcttaatgtttacacgatggtagtaga-ataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcattt-ttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
                                                                                         ||||  ||| |  |  |     || |  |  |   ||  |       ||| ||  |||  |||   || | | ||  |   ||   ||  || ||| ||||| ||||||||||||||||| || ||||| |||||||| || ||||| || |||||||| ||  || |  |   | | |||||||||||||||
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctca-agtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
                    aactaac  putative branch site (score: 1)
                                    catttttcattctct  putative PPT
           ttttcttttaactaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttaatgtttacacgatggtagtagaataatgaatatgatcatagcgttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA