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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTCAGACAGACATGGAAACACAAATACATGAGCTTGAGCAAGAAGCATATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgtacactcttgtctcttcatgtaattaatttatttactctggttggcctagatttcatggagtcttgtaagggtttgaattcattgtctcag

Basic information

species Zea mays
transcript GRMZM5G838910_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G838910_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g23930.1 (Oryza sativa), 5'ss of exon 2
ACCTCAGACAGACATGGAAACACAAATACATGAGCTTGAGCAAGAAGCATATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgta------cact----cttgtctcttcatgtaattaatttatttactc--tggttggcctagatttcatggagtcttgtaaggg-----tttgaattcattgtctcag
 || |||||||| |||||||||||||| ||| ||||||||||||| ||||||||||| |||||| | ||||| || || ||||||||||||||  ||||||||      ||||      ||||  |     |  | | ||  | || ||  | |  |  ||   || |    |       ||  |     ||||||||||   |||   
GCCACAGACAGATATGGAAACACAAATTCATCAGCTTGAGCAAGATGCATATTGTTCTGTTCTTCGTGCATTTAAAGCACAATCTGATGCTATTTCATGGgtaaaacaccacttaactctgtcattcttcatcttcatttggtgtaatcgttagcagttcttttttccgcaaaactgaccaaaagacaattttgaattcaacttctag-

upper sequence: GRMZM5G838910_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G39100.1 (Glycine max), 5'ss of exon 1
ACCTCAGACAGACATGGAAACACAAATACATGAGCTTGAGCAAGAAGCATATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgtacactcttgtctcttcatgtaattaatttatttactctg---gttggcctagatt-tcatggagtcttgtaagggtttgaattcattgtctcag
    ||||  ||||||||||||||||| ||| |  ||||||||||||||||    || || ||  | || || || |||||||||||||| || || |||||||  |    ||  ||||| |  ||  | | | || |  |   || ||    ||||  ||  ||||  | |    |||   ||  | | |     
GATGCAGAACGACATGGAAACACAAATCCATAACATTGAGCAAGAAGCATACACCTCTGTCCTGCGGGCTTTTAAAGCTCAATCTGATGCAATCACTTGGgtacctttgcctcaattcat-tggtttgtctttctattaagtatgtcggataggattgccaatgagttcttt---tgttcctatgtactttag---

upper sequence: GRMZM5G838910_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G36910.1 (Glycine max), 5'ss of exon 2
ACCTCAGACAGACATGGAAACACAAATACATGAGCTTGAGCAAGAAGCATATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgtacactcttgtctcttcatgtaattaatttatttactctggttggcctagatttcatggagtcttgtaagggtttgaattcattgtct-cag
   | | |  || ||||| || ||||| ||| |||||||||||||||||||  |||||||||| ||||| || || |||||| | ||||| || || ||||||   | || | ||||  |  |   ||| || |   | ||  |  | |  |||   || |      |     ||   ||  ||| ||| |||
CGGTGAAATTGATATGGAGACCCAAATTCATCAGCTTGAGCAAGAAGCATACAGTTCAGTTCTAAGAGCTTTTAAAGCTCAAGCCGATGCCATTACTTGGgtatg-ttttatatcttgtttcatcaaatatagtatttttgaatt-cttttattaggtgtaagtgactgctacttgacatgtattttcttcag

upper sequence: GRMZM5G838910_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G02360.1 (Glycine max), 5'ss of exon 1
------------------------------------------ACCTCAGACAGACATGGAAACACAAATACATGAGCTTGAGCAAGAAGCATATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgtacactcttgtctcttcatgtaattaatttatttactctggttggcc-tagatttcatggagtcttgtaagggtttgaattcat-tgtctcag
                                              ||||  ||||||||||||||||| ||| |  ||||||||||||||||    || || || |  || || || |||||||||||||| || || |||| ||  |    |   ||||| |  ||  | | | || |  |  || |  |||  ||      |  || |     ||||     || |   | ||
AAACGGAAGATCTGCAATTGTAGGCTCTGGTCCATATCCTCGGATGCAGAACGACATGGAAACACAAATCCATAACATTGAGCAAGAAGCATACACCTCTgtcctgaaggcttttaaagctcaatctgatgcaatcacttgggcacctttgccttaattcat-tggtttgtctttctattaagtatgtcgataggattggcaatgagtttt-----tttgttcctatgtactttag

upper sequence: GRMZM5G838910_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G00250.3 (Glycine max), 5'ss of exon 2
ACCTCAGACAGACATGGAAACACAAATACATGAGCTTGAGCAAGAAGCATATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgtacactcttgtctcttcatgtaattaatttat--ttactctggttggcctagatttcatggagtcttgtaagggtttgaattcattgtct-cag
   | | |  || ||||| || ||||| ||| |||||||||||||||||||  |||||||||| ||||| || || |||||| | ||||| || || ||||||   | |    ||||  |  |   ||| ||   ||  |    ||     | |  |    | | ||  |     ||   ||   || ||| |||
TGGTGAAATTGATATGGAGACCCAAATTCATCAGCTTGAGCAAGAAGCATACAGTTCAGTTCTAAGAGCCTTTAAAGCTCAAGCCGATGCCATTACTTGGgtatgttttataatcttgtttcatcgaatatagcattttttgaattttttaataggtgtaagtgactgctgctacttcacatgtgttttcttcag

upper sequence: GRMZM5G838910_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0156g00360.t01 (Vitis vinifera), 5'ss of exon 2
ACCTCAGACAGACATGGAAACACAAATACATGAGCTTGAGCAAGAAGCATATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgtacactcttgtctcttcatgtaattaatttatttactctggttggcctagatttcatggagtcttgtaagggtttgaattcattgtctcag------
   | | || || ||||| || ||||| ||  | || ||||||||||||||| |||||||| | ||||| ||||| |||||| ||||||| || || |||||||  |  ||||  ||  | |   | |      || |||    ||  |   ||| |    || | ||||  | |  ||| || ||| |         
TGGTGAAACTGATATGGAGACCCAAATTCACCAACTAGAGCAAGAAGCATATAGTTCAGTTTTAAGAGCCTTCAAAGCTCAAGCTGATGCCATTACTTGGgtacttttctgtcattttgtttgcatgaacctaatattctaa--ggaattttttttaccaggtttagtaactgct-aaatgcaatgttttttcttcag

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|40336552|gb|CK370622.1|CK370622
EST:     GATGCTATTACATGG                         GAAAAAGAAAGTCTCATTACTGAGCTTAGGAAGGAGCTACAAGTATCTGAC
genomic: GATGCTATAACATGGgtacactctt ... attgtctcagGAAAAAGAAAGTCTCATTACTGAGCTTAGGAAGGAGCTACAAGTATCTGAC
EST: gi|74232209|gb|DT640123.1|DT640123
EST:     ATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGG                         GAAAAAGAAAGTCTCATTACTGAGCTTAGGAAGGAGCTACAAGTATCTGAC
genomic: ATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgtacactctt ... attgtctcagGAAAAAGAAAGTCTCATTACTGAGCTTAGGAAGGAGCTACAAGTATCTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTCAGACAGACATGGAAACACAAATACATGAGCTTGAGCAAGAAGCATATTGTTCAGTTCTTAGAGCATTCAAGGCTCAATCTGATGCTATAACATGGgtacactcttgtctcttcatgtaattaatttatttactctggttggcctagatttcatggagtcttgtaagggtttgaattcattgtctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA