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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgatagcttggtgcatgactgcatggtttttagattttgaagtagatcctattaaatatcaatttatatcttattaaatacaaatttcgaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTACTGATGACCTCCTCCTGCAAGGCCTACGGAAATGCAAGTCGCTTGGTGC

Basic information

species Zea mays
transcript GRMZM2G020002_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g59340.3 (Oryza sativa), 3'ss of exon 7
tttgatagcttggtgcatgactgca-tggtttttagattttgaag--tagatcctattaaatatcaatttatatcttattaaatacaaatt-tcgaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTACTGATGACCTCCTCCTGCAAGGCCTACGGAAATGCAAGTCGCTTGGTGC
   |  |  ||  || | | ||||| ||  | | |||   ||| |  | | | ||||    ||||    | ||  |     |||  |||||  | | ||| ||||||| |||||||||||||| |||||||| |||||||| || |||||||| || |||||||| |||||||||||| ||| ||||||||| || ||||||||
---gcaaatttcctgta-gtctgcaatgtctatcagaacatgatgctttggtactatattgtatcgtagtctaagtgccagaatttaaattgccaatatttcagGGATCAATTCTTTCAAGTTCTTCATGGCGTATAAAGGTTCATTGATGGTCACGGATGACCTACTCCTGCAAGGCTTACAGAAATGCAAATCTCTTGGTGC

upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 4
---------------tttgatagcttggtgcatgactgcatggtttttagattttgaagtagatcctattaaatatcaatttatatcttattaaatacaaatttcgaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTACTGATGACCTCCTCCTGCAAGGCCTACGGAAATGCAAGTCGCTTGGTGC
                ||||||  || |    | | |   |||   | |   ||||  || ||   |||     ||  ||||  ||||  |  |       ||| | ||||||||| |  || ||||| |||||||||||||||||||||||  |  | ||| | | ||||||  | || ||| ||||  |    || |||||||| ||||||||
gtcataatttatttccttgataatttagc---taattatgtggaaataaccctttg--gttgagtttatggggaatttattt-catctagtgcatctatgtttttgtaattgcagGTACCAACTCTTTTAAGTTTTTCATGGCATATAAAGGAGCTCTTATGATCAATGATGAGTTTCTTCTGGAAGGATTTAAAAAGTGCAAGTCTCTTGGTGC

upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 4
tttgatagcttggtgcatgactgcatggtttttagattttgaagtagatcctattaaatatcaatttatatcttattaaatacaaatttcgaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTACTGATGACCTCCTCCTGCAAGGCCTACGGAAATGCAAGTCGCTTGGTGC
                     ||  |  ||| |   ||      |  ||  | | | |  |   || ||    |  || ||  |  ||| | |||||||||||| || ||||| ||||||||||||||||| |||||     | ||| | | |||||| || || ||| ||||  |    ||||||||||| ||||||||
-------------------gttgt-tattttattatttccttgatgcatttt-tgataatttggttgattgggtggtacatctatgttttgtaattgcagGGATCAACTCTTTTAAGTTTTTCATGGCATACAAAGGAATTCTTATGATCAATGATGAGCTTCTTCTGAAAGGATTTAAAAAATGCAAGTCTCTTGGTGC

upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 4
---------------tttgatagcttggtgcatgactgcatggtttttagattttgaagtagatcctattaaatatcaatttatatcttattaaatacaaatttcgaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTACTGATGACCTCCTCCTGCAAGGCCTACGGAAATGCAAGTCGCTTGGTGC
                ||||||  ||||    ||| |   |||   | |   ||||   | ||   |||     ||  ||||      ||||  ||  |  ||| | ||||||||| || || ||||| ||||||||||||||||| |||||  |  | ||| | | |||||| || || ||| ||||  |    || |||||||| ||||||||
gtcatgatttatttccttgataatttggc---tgattatgtggcaataaccctttggttttgagtttatgtggaatttatttcagc--tattgcatctatgttttgtaattgcagGCATCAACTCTTTTAAGTTTTTCATGGCATACAAAGGAGCTCTTATGATCAATGATGAGCTTCTTCTGGAAGGATTTAAAAAGTGCAAGTCTCTTGGTGC

upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 4
----------------------------tttgatagcttggtgcatgactgcatggtttttagattttgaagtagatcctattaaatatcaatttatatcttattaaatacaaatttcgaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTACTGATGACCTCCTCCTGCAAGGCCTACGGAAATGCAAGTCGCTTGGTGC
                            |||||||  |||||   ||| |   ||||  | |   ||||  ||   |  ||  |||| | | |  |  |   | || ||  |  ||| | |||||||||||| || ||||| ||||||||||||||||| |||||     | ||| | | |||||| || || ||| ||||  |    ||||||||||| ||||||||
gttgttatttattatttccttgctgcattttgataatttggt---tgattaggtggtagtaaccctttgg-gtgagttgtaagaaat-ttattccaggt---agtacatctatgttttgtaattgcagGGATCAACTCTTTTAAGTTTTTCATGGCATACAAAGGAATTCTTATGATCAATGATGAGCTTCTTCTGGAAGGATTTAAAAAATGCAAGTCTCTTGGTGC

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|149082368|gb|EE171552.2|EE171552
EST:     GTGGAATGATGAGGTTGCAAGGGAAATGGAAGTGATGGTTAAAGAACATG                         GGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTA
genomic: GTGGAATGATGAGGTTGCAAGGGAAATGGAAGTGATGGTTAAAGAACATGgtcagtgtat ... gaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTA
EST: gi|31355355|gb|CD439712.1|CD439712
EST:     GTGGAATGATGAGGTTGCAAGGGAAATGGAAGTGATGGTTAAAGAACATG                         GGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTCA
genomic: GTGGAATGATGAGGTTGCAAGGGAAATGGAAGTGATGGTTAAAGAACATGgtcagtgtat ... gaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatcctattaaatatcaatttatatcttattaaatacaaatttcgaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTACTGATGACCTCCTCCTGCAAGGCCTACGGAAATGCAAGTCGCTTGGTGC
      tattaaatatcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgatagcttggtgcatgactgcatggtttttagattttgaagtagatcctattaaatatcaatttatatcttattaaatacaaatttcgaaattgcagGGATAAATTCTTTCAAGTTTTTCATGGCATATAAAGGCTCCTTGATGGTTACTGATGACCTCCTCCTGCAAGGCCTACGGAAATGCAAGTCGCTTGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - -tgcatga
- - - - - - - - - - -tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacaaa