This page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.

Genomic Sequence Homology

To elucidate the evolutionary history of the human GRM7 gene, candidate orthologs and paralogs were identified. To identify candidate orthologs, "GRM7" was queried on the homologene website. Additionally, candidate orthologous genes were inferred using a BLAST search on Wormbase and FlyBase for proteins similar to the human GRM7 isoform a protein, and then finding the gene corresponding to the protein. Candidate orthologs of the human GRM7 gene were found in animals ranging from nematodes to fruit flies to mice. No candidate orthologs of the GRM7 gene were found in plants or bacteria, perhaps because, unlike animals, these organisms do not have a nervous system, and therefore, would not need a neurotransmitter receptor like the GRM7 protein.
Candidate paralogs of the human GRM7 gene were identified by searching the GRM7 isoform a protein sequence against RefSeq protein on the BLAST human sequences website, and then finding the corresponding genes. Not suprisingly, candidate paralogs of the GRM7 gene include the entire family of GRM genes. Two other genes, CASR and TAS1R2, were also identified as candidate paralogs through protein similarity using the BLAST human sequences website
. Whether these genes truly represent paralogs remains uncertain; however, they will be included in all analyses involving homologs of GRM7 conducted for this project.

Orthologs of Genomic Sequence

Table 1. Candidate orthologs of the GRM7 gene. For each candidate orthologous gene, the table gives the organism in which it is found, the name of the gene, the accession number (with a link to the GenBank entry for that gene), the GI number, the size of the gene, and  where in the genome of the organism the gene is located (Entrez Gene, 2008 and 2009).

Organism

 

Organism

Gene Name

Gene Accession Number

GI Number

Gene Size

Chromosomal Location

Homo sapiens (human)

GRM7 glutamate receptor, metabotropic 7

NC_000003.10 (6877927..7758217)

89161205

880291 bp

3p26.1-p25.1

Pan troglodytes (chimpanzee)

GRM7 glutamate receptor, metabotropic 7

NC_006490.2 (7050647..7947370)

114796132

896724 bp

3

Mus musculus (mouse)

Grm7 glutamate receptor, metabotropic 7

NC_000072.5 (110595592..111517224)

149361431

921633 bp

6 E3

Rattus norvegicus (rat)

Grm7 glutamate receptor, metabotropic 7

NC_005103.2 (146952340..147270225)

62750804

317886 bp

4q42

Canis lupus familiaris (dog)

GRM7 glutamate receptor, metabotropic 7

NC_006602.2 (13283748..14060928, complement)

74033247

777181 bp

20

Gallus gallus (chicken)

GRM7 glutamate receptor, metabotropic 7

NC_006099.2 (19495863..19700556)

118135638

204694 bp

12

Danio rerio (zebrafish)

zgc:158329

NC_007122.3 (22861257-22906349)

189908152

45093 bp

11

Caenorhabditis elegans (nematode)

mgl-1 Metabotropic Glutamate receptor family

NC_003284.7 (9968563..9974336, complement)

193211360

5774 bp

X

Drosophila melanogaster (fruit fly)

mGluRA metabotropic glutamate receptor

NC_004353.3 (957468..967451)

116010290

9984 bp

102C5-102C6

 

Paralogs of Genomic Sequence

Table 2. Candidate paralogs of the GRM7 gene. For each candidate paralogous gene, the table gives the name of the gene, the accession number (with a link to the FASTA format sequence for that gene), the GI number, the size of the gene, and  where in the human genome the gene is located (Entrez Gene, 2009).

Gene Name

 

Gene Name

Gene Accession Number

GI Number

Gene Size

Chromosomal Location

GRM7 glutamate receptor, metabotropic 7

NC_000003.10 (6877927..7758217)

89161205

880291 bp

3p26.1-p25.1

GRM1 glutamate receptor, metabotropic 1

NC_000006.10 (146392112-146800427)

89161210

408316 bp

6q24

GRM2 glutamate receptor, metabotropic 2

NC_000003.10 (51718004-51727669)

89161205

9666 bp

3p21.1

GRM3 glutamate receptor, metabotropic 3

NC_000007.12 (86111166-86332128)

89161213

220963 bp

7q21.1-q21.2

GRM4 glutamate receptor, metabotropic 4

NC_000006.10 (34209421-340976060, complement)

89161210

111816 bp

6p21.3

GRM5 glutamate receptor, metabotropic 5

NC_000011.8 (88420838-87880626, complement)

51511727

540213 bp

11q14.2-q14.3

GRM6 glutamate receptor, metabotropic 6

NC_000005.8 (178354730-178337934, complement)

51511721

16797 bp

5q35

GRM8 glutamate receptor, metabotropic 8

NC_000007.12 (126670548-125865895, complement)

89161213

804654 bp

7q31.3-q32.1

CASR calcium-sensing receptor

NC_000003.10 (123385220-123488032)

89161205

102813 bp

3q13

TAS1R2 taste receptor, type 1, member 2

NC_000001.9 (19058742-19038680, complement)

89161185

20063 bp

1p36.13

 

References

References

 

Entrez Gene. (2008). GRM7 glutamate receptor, metabotropic 7 [Canis lupus familiaris]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=484674

Entrez Gene. (2008). mgl-1 Metabotropic GLutamate receptor family [Caenorhabditis elegans]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=191707.

Entrez Gene. (2009). calcium-sensing receptor [Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=37577159[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=14.

Entrez Gene. (2009). glutamate receptor, metabotropic 1[Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=166999098[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=13.

Entrez Gene. (2009). glutamate receptor, metabotropic 2 [Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=66529100[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=8.

Entrez Gene. (2009). glutamate receptor, metabotropic 3 [Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=46358417[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=7.

Entrez Gene. (2009). glutamate receptor, metabotropic 4 [Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=4504141[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=5.

Entrez Gene. (2009). glutamate receptor, metabotropic 5 [Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=4504143[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=10.

Entrez Gene. (2009). glutamate receptor, metabotropic 6 [Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=110611176[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=6.

Entrez Gene. (2009). glutamate receptor, metabotropic 8 [Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=187960067[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=3.

Entrez Gene. (2009). GRM7 glutamate receptor, metabotropic 7 [Gallus gallus] . Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=416112.

Entrez Gene. (2009). GRM7 glutamate receptor, metabotropic 7 [Homo sapiens]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=2917.

Entrez Gene. (2009). Grm7 glutamate receptor, metabotropic 7 [Mus musculus] . Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=108073.

Entrez Gene. (2009). GRM7 glutamate receptor, metabotropic 7 [Pan troglodytes]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=460140.

Entrez Gene. (2009). Grm7 glutamate receptor, metabotropic 7 [Rattus norvegicus]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=81672.

Entrez Gene. (2009). mGluRA metabotropic glutamate receptor [Drosophila melanogaster]. Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=43838.

Entrez Gene. (2009). taste receptor, type 1, member 2. [Homo sapiens]. Retrieved February 28, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=112789566[PUID]&RID=UKA0ZMG6016&log%24=genetop&blast_rank=15.

Entrez Gene. (2009). zgc:158329 zgc:158329 [Danio rerio] . Retrieved February 27, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=565450.

Jennifer Wagner
wagner4@wisc.edu
Updated February 27, 2009
http://www.gen677.weebly.com