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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttagtggatattttgtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG

Basic information

species Zea mays
transcript GRMZM2G003157_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 16
-----cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttagtggatattttgtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG
     | |||     |  || || |  |    | | ||| ||     ||   ||  | | |   | |   | |     | |||| | | ||     ||| ||||||||||||| ||||| || |||||||||||||| ||||||||||||||||||||||||||||||||| || | ||
ttaaacatcaagaagtacatatcttccagagca-tatacttg--acttgctgcatagtactggtggattctctgtagatacttatttg-taccc-atttttgcagATGGTTGGTGATTTTTTCGATCAACTGAAATCTCGAAGTAAAGGATATGCTAGCATGGAATATTCACTTATCGG

upper sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 11
cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttagt-ggatatttt--------gtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG
  | | ||  || |||  |||  ||   ||  |||   | ||            || ||  |  |||  || |    || | | |||||||          || || |||||||||| ||||||||||| ||  |||| ||  ||||||| || |||||||||||||| ||| |  |||| ||
-gtaatctcttgcatta-gttcttgtctattgaccctaaaaactcgtgcttctgtttaactagttttggctctcaagtatttgaatatttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCTAGCATGGAGTATACCTTTGTCGG

upper sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 16
cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttag-tggatatttt--------gtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG
  | | ||  || |||  |||  ||  |||  |||   | ||   |        ||  |  |  |||  || |     |  || || ||||          || || |||||||||| ||||||||||| ||  |||| ||| ||||||| || |||||||| ||||| ||| |  |||| ||
-gtaatctcttgcatta-gttcttgtcaattgaccctaaaaactcatgcttctgtttgactagttttggctctcaagcatctgaatctttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCTAGTATGGAGTATACCTTTGTCGG

upper sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 16
------cttcagctgatgta---tttcgttgatgctaatgtacctgtaga-atgtaccaaggaattaaagaaaattttcctattgcttagtggatattttgtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG
        || |||  || |   ||  | | |  | |||| |  | |||  ||||  |     ||||   ||| |  || | ||| | |  |     |    || |||||||||| || ||||||||||| ||| |||| ||  |||  || |||||||||||||||||||| || ||| ||||
gtgagatctctgcttgtgcagagttaagataaccccaatgaaagtttagccatgtctctcttgattatgtaaactgatcttcttgttaatcgctccctgccattttgcagATGGTGGGTGATTTCTTTGACCAATTGAAGTCGAGAACCAAGGGATATGCTAGCATGGAATACTCCGTTATTGG

upper sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 16
lower sequence: EFJ32321 (Selaginella moellendorffii), 3'ss of exon 16
cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttagtggatattt--tgtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG
                                                |  | | |    |  |||||| |  |||||    |   |||    |||  | |||||||||| ||||||||||||||| |||| ||||| || || || || || |||||||| || ||  ||   ||
----------------------------------------------gtacagtactctcaagcattttctt-ctgcttgaatgccgtttaacattttggtagATGGTTGGAGATTTCTTTGATCAATTGAAGTCACGTAGCAAGGGCTACGCGAGCATGGAGTACTCCATTACCGG

upper sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 16
lower sequence: EFJ20933 (Selaginella moellendorffii), 3'ss of exon 16
cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttagtggatattttgtttgt--gcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG
                                                |  | | |    |  |||| | |  |||||    |   |||    | |  | |||||||||| ||||||||||||||| |||| ||||| || || || ||||| |||||||| || ||  ||   ||
----------------------------------------------gtacagtactctcaagcatttgctt-ctgcttgaatgccgtttaaccttttggtagATGGTTGGAGATTTCTTTGATCAATTGAAGTCACGTAGCAAGGGCTATGCGAGCATGGAGTACTCCATTACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaaggaattaaagaaaattttcctattgcttagtggatattttgtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG
                                         ttttgttt  CT-rich tract
       aattaaagaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttagtggatattttgtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - -gctgatg
- - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - acctgta
- - - - - - - - - - - - - - - - - - - - - tgtacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa