click on above figure to see a larger version
The GGCCCATTA motif was next examined to see its position distribution upstream of the start of the gene. The figure in the lower left of this panel shows the distribution of GGCCCATTA, as well as TAATGGGCC (its inverse sequence) with up to one mismatch. As this graph demonstrates, this sequence is preferentially found about 100 to 200 bases upstream of the gene start.
click on above figure to see a larger version
The orientation of this element did not seem to make a difference in its distribution. We then examined the set of genes for which this motif is found. We only considered exact matches for this search, the results of which are shown in this table.
| Number | Category |
| 331 | total number of loci with GGCCCATTA motif |
| 178 | number of genes with some identified function |
| 31 | translation and protein delivery |
| 18 | transcription factors and other DNA binding proteins |
| 9 | RNA splicing related |
| 9 | DNA replication related |
Of the 331 genes identified, only 178 had identified functions. These genes seemed to contain many examples of products involved in the flow of genetic information. The list below shows those genes which have been identified in the table above.
| Identifiable Genes With GGCCCATTA Motif | |
| Translation and Protein Delivery Related (31) | |
| At2g19750 | 40S ribosomal protein S30 |
| AT3g49910 | 60S RIBOSOMAL PROTEIN - like 60S RIBOSOMAL PROTEIN L26 |
| At2g18020 | 60S ribosomal protein L2 |
| AT5g27770 | 60S ribosomal protein L22 - like ribosomal protein L22 (cytosolic |
| At2g39460 | 60S ribosomal protein L23A identical to GB:AF034694 |
| AT5g56710 | 60S ribosomal protein L31 |
| AT3g28500 | acidic ribosomal protein P2b (rpp2b |
| At1g14980 | chaperonin CPN10 identical to SP:P34893 from [Arabidopsis thaliana |
| AT5g02490 | hsc70.1 - like dnaK-type molecular chaperone hsc70.1 |
| AT5g44320 | eukaryotic translation initiation factor 3 subunit 7 |
| AT5g06000 | eukaryotic translation initiation factor 3 subunit-like protein |
| AT4g10320 | isoleucine-tRNA ligase - like protein isoleucine--tRNA ligase |
| AT4g39460 | mitochondrial carrier - like protein AgPET8 |
| AT5g53180 | polypyrimidine tract-binding RNA transport protein-like |
| At2g18110 | putative elongation factor beta-1 /51228.m00082#T27K22.2 |
| AT3g09500 | putative 60S ribosomal protein L35 similar to 60S ribosomal protein L35 GB:AAC27830 |
| At2g40660 | putative methionyl-tRNA synthetase |
| At2g18710 | putative preprotein translocase SECY protein Identical to GB:U37247; targeted to the thylakoid membrane; the protein has a chloroplast targeting signal |
| AT3g63190 | putative protein chloroplast ribosome recycling factor protein - Spinacia oleracea |
| AT4g26310 | putative protein elongation factor P (efp) RP238 |
| At2g17980 | putative SEC1 family transport protein similar to SLY1 proteins and vesicle transport proteins |
| AT3g06540 | Rab escort protein |
| At1g07070 | ribosomal protein |
| AT3g25520 | ribosomal protein |
| At1g32990 | ribosomal protein L11 |
| AT3g54210 | ribosomal protein L17 -like protein ribosomal protein L17 |
| AT5g02610 | ribosomal protein L35 - like ribosomal protein L35- cytosolic |
| AT5g20160 | ribosomal protein L7Ae-like NHP2/RS6 FAMILY PROTEIN YEL026W HOMOLOG - Homo sapiens |
| AT4g29390 | RIBOSOMAL PROTEIN S30 homolog |
| At1g48900 | signal recognition particle 54 kDa protein 2 (SRP54 |
| AT5g49500 | SRP54 (signal recognition particle 54 KDa) protein |
| Transcription Factors and other DNA binding proteins (18) | |
| At1g72050 | C2H2-type zinc finger protein |
| AT3g53650 | histone H2B - like protein histone H2B-2 |
| AT3g46030 | histone H2B -like protein histone H2B1 |
| AT5g59970 | histone H4 - like protein histone H4 |
| At1g54230 | hypothetical protein contains similarity to histone H1 GI:11558847 from [Triticum aestivum |
| At1g20280 | hypothetical protein contains similarity to homeobox-leucine zipper proteins |
| At2g36740 | hypothetical protein predicted by genscan; similar to DNA-binding protein YL-1 |
| At1g78760 | hypothetical protein similar to heat shock transcription factor like protein GI:7268102 from [Arabidopsis thaliana |
| AT3g09480 | putative histone H2B similar to histone H2B-3 GB:CAA12231 from [Lycopersicon esculentum |
| At1g10230 | putative kinetochore protein similar to kinetochore (SKP1p)-like protein (gi|3548811); similar to EST gb|T42880 |
| AT5g51910 | putative protein contains similarity to DNA binding protein PCF1 |
| AT5g09450 | putative protein DNA-binding protein - Triticum aestivum |
| AT5g02570 | putative protein histone H2B-2 |
| AT3g05060 | putative SAR DNA-binding protein-1 similar to GB:AAC16330 from [Pisum sativum |
| AT3g06010 | putative transcriptional regulator similar to homeotic gene regulator (brahma protein); contains Pfam profile PF00176 SNF2 and others N-terminal domain |
| AT5g23090 | TATA-binding protein-associated phosphoprotein Dr1 protein homolog (sp|P49592 |
| At1g75510 | transcription initiation factor |
| At1g61570 | unknown protein similar to small zinc finger-like protein GI:5107149 from [Oryza sativa |
| Splicing Related (9) | |
| AT3g61860 | ARGININE/SERINE-RICH SPLICING FACTOR RSP31 |
| AT3g11964 | hypothetical protein similar to putative pre-rRNA processing protein GB:AAF23213 |
| At1g09140 | putative SF2/ASF splicing modulator |
| At2g18510 | putative spliceosome associated protein |
| At2g14550 | putative spliceosome associated protein |
| AT4g30220 | snRNP Sm protein F - like Sm protein F |
| At1g23860 | splicing factor |
| At1g14650 | splicing factor |
| At1g60170 | unknown protein contains similarity to splicing factor required for vegetative and meiotic growth GI:2959374 from [Schizosaccharomyces pombe] |
| DNA Replication Related (9) | |
| AT5g11200 | DEAD BOX RNA helicase RH15 |
| AT5g11170 | DEAD BOX RNA helicase RH15 - like protein DEAD BOX RNA helicase RH15 |
| AT5g67100 | DNA polymerase alpha 1 |
| AT5g41880 | DNA polymerase alpha subunit IV (primase)-like protein |
| At1g34380 | DNA polymerase type I |
| At1g03750 | hypothetical protein similar to DNA Helicases and DNA repair proteins |
| At2g02090 | putative helicase |
| At1g79890 | putative helicase similar to helicase GB:AAB06962 [Homo sapiens |
| At1g33680 | single-strand nucleic acid-binding protein |
| Abstract | ||
| Panel 1 | Panel 3 | Panel 5 |
| Panel 2 | Panel 4 | Panel 6 |