Question

Gene is: LOC_Os05g38000

1. The gene name and chromosomal location. (Oryzabase)
2. Number of exons and introns. (RGAP)
3. Describe the expression pattern. This will require some research as there is no convienent Atlas.

Can someone please help with this question!

Answer 1

Geneticists use a standardized way of describing a gene's cytogenetic location. In most cases, the location describes the position of a particular band on a stained chromosome

Gene Structure

Gene Attributes
Chromosome:	Chr5
CDS Coordinates (5'-3'):	22293497 - 22297207
Nucleotide length:	1707
Predicted protein length:	569
Predicted molecular weight:	62303.6

Gene Annotation

Total loci	55,986
Non-TE Loci
Number	39,045
Gene models	49,066
Gene size	2,853 bp
Exons/gene	4.9
Introns/gene	3.9
TE Loci
Number	16,941
Gene models	17,272
Gene size	3,223 bp
Exons/gene	4.2
Introns/gene	3.2

The combination of numbers and letters provide a gene's “address” on a chromosome. This address is made up of several parts:

• The chromosome on which the gene can be found. The first number or letter used to describe a gene's location represents the chromosome. Chromosomes 1 through 22 (the autosomes) are designated by their chromosome number. The sex chromosomes are designated by X or Y.

• The arm of the chromosome. Each chromosome is divided into two sections (arms) based on the location of a narrowing (constriction) called the centromere. By convention, the shorter arm is called p, and the longer arm is called q. The chromosome arm is the second part of the gene's address. For example, 5q is the long arm of chromosome 5, and Xp is the short arm of the X chromosome.

• The position of the gene on the p or q arm. The position of a gene is based on a distinctive pattern of light and dark bands that appear when the chromosome is stained in a certain way. The position is usually designated by two digits (representing a region and a band), which are sometimes followed by a decimal point and one or more additional digits (representing sub-bands within a light or dark area). The number indicating the gene position increases with distance from the centromere. For example: 14q21 represents position 21 on the long arm of chromosome 14. 14q21 is closer to the centromere than 14q22