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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT

Basic information

species Zea mays
transcript GRMZM2G406553_T04
intron # 1
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 1
-tgtctgaagtggtacattgatgtaaatgatgttagttatc-gggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
 ||  | | |   | |  ||| |      |  | | ||||  ||||| ||||  |  | | ||  ||| ||||||  ||||||||||||||| |||| ||||||||||||||||||||| | |||||||| |||||||||||||||||||||||||| ||||| ||||| || || |||||||| || |||||||| |||||
gtgctt-atgaactgc-ctgaagattgcaacatgatttatttgggggtgattttgtgggtgaacttgcgacattggaatgccttgacttgcgtttggcgtagAGGAGTTTGTGGCGCATTCATCCAATGTCAACTGCCTCAAGATTGGGAGGAAGACTTCACGAGTTCTCGTGACAGGAGGAGATGACCATAAGGTTAATCT

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgc-taaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
                                                                    | |  |   | | ||   | |  |   ||||| ||||    |    ||    ||  |   ||||  || | ||   ||||||||  |  ||  ||  |||||| ||||| || ||||| || | ||| || ||||||||||||||  ||||  | ||  ||||||||||||| ||||| || ||||| |||||||||||
gtatccttcatctcttgtctgtctgtgctttacattttgtttgatctatctatgcactcgcccttcattttctatctgcagatctctctctactttgtta-ttatgttagagtctttctttgtgtgtgtgtgtgacttggctg-gccttgacgagttat--gtccagAGGAATTTGTAGCACATGCTTCTACTGTCAATTGCCTCAAGATTGGACGGAAATCATCCAGGGTTCTTGTCACTGGAGGTGAAGATCACAAGGTCAATCT

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
tgtctgaag-----tggtacattgatg-taaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgact-tgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
  |||| ||     |  |  |    || |  |     || |||||   |  |  |||   |  ||  | |    |      || |||||||   |   || |   |||||| ||||| || ||  | |||| ||| ||||| |||||||||||||||||| | ||  |||||||||||||||| ||||| ||||| ||||| |||||
--tctgcagatcccttctctacccttgcttcacagcatttgttattttga-attttgaatttttacttct----cgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S101_210V6.1 (Physcomitrella patens), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggag--attgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
  ||| |   |    |    |  ||||  | | ||| ||    |     |||||   |   | |||   |    |    | | |    | | |    |  |||||||||||| || ||  | |||||||| ||||||||||||||||||| |||| ||||  ||||  | |||||||| ||||||||||| || |||||  |
aatcttattagtctaaacactccaaattgt-tgagtcatttacgtgcttattggtgaggatattgtataattcggtttagtccttgactactaccctt-cagAGGAGTTTGTTGCACACTCTTCCAATGTCAACTGCCTCAAGATTGGGAAGAAGTCCTCTAGGGTCTTGGTCACCGGCGGAGAGGATCACAAAGTCAACAT

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S9_241V6.1 (Physcomitrella patens), 3'ss of exon 1
------tgtc-tgaagtggtacattga-tgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
      | || |||  | |||  |  | ||| | || ||| | ||    |    |||   | ||||   ||  ||| ||   | | ||||||||      |  || |||||| ||||| ||||| |||||| |||| ||||||||||| ||||| | |||| ||||  |||| || ||||| || || |||||||| || || ||  |
gtaaaatatcatgatttcgtatttcaactgtgattgttgtcattt---cgtctcgatgaagttgctg--tggtccagatcatg-ttccttgactactagat--tgcagAGGAATTTGTTGCGCACGCGTCCGATGTCAACTGCCTCAAAATTGGAAAGAAGTCCTCCAGGGTCCTGGTCACGGGCGGGGAGGATCACAAAGTTAACAT

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ05569 (Selaginella moellendorffii), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
                              || ||||     |    ||| |  |  |   |  |     |||      ||||  |||       |  |||||||||||| |||||| | ||| | ||||| ||||||||||| |||||||| || || ||||| ||                                 
------------------------------gtgagtttcttcg---catttgatttttttttcagAGCTTTTGGTTGATCTTG--TTGGTGGCAATCCAGAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCT---------------------------------

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ26184 (Selaginella moellendorffii), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
                              || ||||     |     | ||  | ||    | ||        |||    |   | || ||      |||||||||||| |||||| | ||| | ||||| ||||||||||| |||||||| || || ||||| || |||||||| ||||| ||||| ||||||||| |
------------------------------gtgagtttcttcgcat--tcggttttctttcagagctgttggttgatcttgttggtggcaatc----cagAGGAGTTTGTTGCGCATTCTTCCCAGGTGAATTGCCTCAAGATCGGGAGGAAAACATCGCGGGTGCTCGTCACCGGTGGAGACGATCACAAGGTCAATAT

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ20167 (Selaginella moellendorffii), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatg---atgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
   ||||    | | | ||| |  |  |   | | |   ||||        ||     | |     |      | |||| |  ||   || | ||| |   |||||| || || || ||||  ||| |||| ||||| || || || ||||  ||  |||||||||| |||||||||||||| |||||||| || || ||  |
-agctgagaaagcagaatgaagcgagcgtacaagctccgtatcctttttttttttttggtttcgctttttctttggcgaagttttcctttaccattagc--agAGGAATTCGTTGCTCATGGATCCGATGTCAACTGTCTTAAAATCGGGAAAAAATCCTCACGGGTGCTTGTCACCGGAGGTGAGGATCACAAAGTGAACAT

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23110 (Selaginella moellendorffii), 3'ss of exon 1
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacatt----gcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
   ||||    | | | ||| |  |  | |   || |  ||       ||    |  |   |  ||    |     |||| |  ||   || | ||| |   |||||| || || || ||||  ||| |||| ||||| || || || ||||  ||  |||||||||| |||||||||||||| |||||||| || || ||  |
aagctgagaaagcagaatgaagcgagcg-tacaagct-ccgtatccttttttttttttggtttcgctttttctttggcgaagttttcctttaccattagc--agAGGAATTCGTTGCTCATGGATCCGATGTCAACTGTCTTAAAATCGGGAAAAAATCCTCACGGGTGCTTGTCACCGGAGGTGAGGATCACAAAGTGAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT
                               tgccttgac  putative branch site 
            taaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctgaagtggtacattgatgtaaatgatgttagttatcgggggagattgggctgctaaatgtgccacattgcgatgccttgacttgcgattggtgtagAGGAGTTTGTGGCGCATGCGTCCAATGTGAACTGCCTCAAGATTGGGAGGAAGACCTCACGGGTTCTTGTCACCGGAGGAGAGGATCATAAGGTCAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT