What is the specific location of gene along a chromosome?

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Nomenclature
External links

Understanding:

• In a eukaryote species there are different chromosomes that carry different genes

Eukaryotic chromosomes are linear molecules of DNA that are compacted during cell division (mitosis or meiosis)

Each chromosome has a constriction point called a

centromere, which divides the chromosome into two sections (or ‘arms’)

The shorter section is designated the p arm and the longer section is designated the q arm

Eukaryotic species possess multiple chromosomes that may differ in both their size and the position of their centromere

Staining chromosomes with particular dyes (e.g. Giemsa stain) will additionally generate unique banding patterns

Each chromosome will carry specific genes and the position of a particular gene on a chromosome is called the locus

The region in which a locus is positioned can be identified via three points of reference:

The first point of reference is a number (or letter) which denotes the chromosome (e.g. 7q31 refers to chromosome 7)
The second point of reference is a letter (p or q) to denote which arm the locus is positioned on (e.g. 7q31 is on the q arm)
The third point of reference is a number corresponding to the G band location (e.g. 7q31 is at the longitudinal position 31)

Gene Locations as Shown by a Chromosome Map

Skill:

• Use of databases to identify the locus of a human gene and its polypeptide product

The locus of a human gene and its polypeptide product can both be identified using a single online resource:

GenBank – a genetic database that serves as an annotated collection of DNA sequences

Identifying Gene Loci

GenBank can be used to identify the specific location of a gene on any given chromosome

To identify a specific gene locus:

Change the search parameter from nucleotide to gene and type in the name of the gene of interest
Choose the species of interest (i.e. Homo sapiens) and click on the link (under ‘Name / Gene ID’)
Scroll to the ‘Genomic context’ section to determine the specific position of the gene locus
A visual profile can be generated by clicking on ‘Map Viewer’ link and looking at the Ideogram on the left side

Identifying Polypeptide Products:

GenBank can also be used to identify the polypeptide product of any given gene

To identify the polypeptide product of a gene:

Change the search parameter from nucleotide to gene and type in the name of the gene of interest
Choose the species of interest (i.e. Homo sapiens) and click on the link (under ‘Name / Gene ID’)
The polypeptide product should be identified within the ‘Summary’ section

Below are examples of different genes that may be searched for:

HBB – Haemoglobin beta gene
DRD4 – Dopamine receptor D4 gene
F8 – Coagulation factor VIII gene
IGF1R – Insulin growth factor 1 receptor gene

Link: Human Genome Online Chromosome Viewer

Location of a gene or region on a chromosome

Parts of a typical chromosome:

(1) Chromatid
(2) Centromere
(3) Short (p) arm
(4) Long (q) arm

In genetics, a locus (plural loci) is a specific, fixed position on a chromosome where a particular gene or genetic marker is located.[1] Each chromosome carries many genes, with each gene occupying a different position or locus; in humans, the total number of protein-coding genes in a complete haploid set of 23 chromosomes is estimated at 19,000–20,000.[2]

Genes may possess multiple variants known as alleles, and an allele may also be said to reside at a particular locus. Diploid and polyploid cells whose chromosomes have the same allele at a given locus are called homozygous with respect to that locus, while those that have different alleles at a given locus are called heterozygous.[3] The ordered list of loci known for a particular genome is called a gene map. Gene mapping is the process of determining the specific locus or loci responsible for producing a particular phenotype or biological trait. Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes (observable characteristics) to genotypes (the genetic constitution of organisms), uncovering genetic associations.

Nomenclature

Cytogenetic banding nomenclature

The shorter arm of a chromosome is termed the p arm or p-arm, while the longer arm is the q arm or q-arm. The chromosomal locus of a typical gene, for example, might be written 3p22.1, where:

3 = chromosome 3
p = p-arm
22 = region 2, band 2 (read as "two, two", not "twenty-two")
1 = sub-band 1

Thus the entire locus of the example above would be read as "three P two two point one". The cytogenetic bands are areas of the chromosome either rich in actively-transcribed DNA (euchromatin) or packaged DNA (heterochromatin). They appear differently upon staining (for example, euchromatin appears white and heterochromatin appears black on Giemsa staining). They are counted from the centromere out toward the telomeres.

Example of cytogenetic bands

Component	Explanation
3	The chromosome number
p	The position is on the chromosome's short arm (a common apocryphal explanation is that the p stands for petit in French); q indicates the long arm (chosen as next letter in alphabet after p; it is also said that q stands for queue, meaning "tail" in French[4]).
22.1	The numbers that follow the letter represent the position on the arm: region 2, band 2, sub-band 1. The bands are visible under a microscope when the chromosome is suitably stained. Each of the bands is numbered, beginning with 1 for the band nearest the centromere. Sub-bands and sub-sub-bands are visible at higher resolution.

A range of loci is specified in a similar way. For example, the locus of gene OCA1 may be written "11q1.4-q2.1", meaning it is on the long arm of chromosome 11, somewhere in the range from sub-band 4 of region 1 to sub-band 1 of region 2.

The ends of a chromosome are labeled "pter" and "qter", and so "2qter" refers to the terminus of the long arm of chromosome 2.

References

^ Wood, E.J. (1995). "The encyclopedia of molecular biology". Biochemical Education. 23 (2): 1165. doi:10.1016/0307-4412(95)90659-2.
^ Ezkurdia, Iakes; Juan, David; Rodriguez, Jose Manuel; Frankish, Adam; Diekhans, Mark; Harrow, Jennifer; Vazquez, Jesus; Valencia, Alfonso; Tress, Michael L. (2014-11-15). "Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes". Human Molecular Genetics. 23 (22): 5866–5878. doi:10.1093/hmg/ddu309. ISSN 1460-2083. PMC 4204768. PMID 24939910.
^ "NCI Dictionary of Genetics". National Cancer Institute. Retrieved 13 December 2014.
^ "NCBI Genetics Review". National Center for Biotechnology Information. Retrieved 10 March 2021.