2. Which of the following best indicates that a segment of DNA is a gene?
a. multiple expressed sequence tags (ESTs) of the DNA sequence
b. 50% identity with a known promoter
c. the DNA sequence is able to form hairpin loop
d. multiple short repeats

The correct answer is (a) multiple expressed sequence tags (ESTs) of the DNA sequence. Multiple independent ESTs mapping to the same genomic segment provide strong evidence that this region is transcribed and therefore corresponds to a gene.​

Introduction

In genomics and CSIR NET–style questions, identifying which DNA segments are true genes is essential for understanding gene structure, expression, and annotation. Among several sequence-based clues, multiple expressed sequence tags (ESTs) aligning to a DNA region are one of the strongest indicators that the segment represents an expressed gene.​

Option (a): Multiple ESTs of the DNA sequence – Correct

Expressed sequence tags (ESTs) are short DNA sequences derived from cDNA, which in turn is synthesized from mRNA; therefore, ESTs represent portions of genes that are actually expressed. When multiple independent ESTs map to the same genomic segment, they provide repeat experimental evidence that this region is transcribed into RNA in real cells or tissues.​

Because ESTs come from mRNA, they preferentially tag exons and coding or expressed regions, making clustered EST hits a powerful way to identify and confirm genes during genome projects and gene discovery efforts. Thus, the presence of multiple ESTs corresponding to a DNA segment best indicates that this segment is a gene.​

Option (b): 50% identity with a known promoter – Incorrect

Promoter sequences control transcription initiation but can vary greatly between genes and species, and even functional promoters often show modest sequence conservation. A 50% identity to a known promoter motif is too low and too nonspecific to reliably indicate that a region is a functional promoter, let alone prove that the entire adjacent DNA segment is a gene.​

Moreover, the presence of a promoter-like sequence only suggests potential regulation, not actual transcription or translation; without expression evidence (such as ESTs or RNA‑seq reads), this is weak support for calling a region a gene.​

Option (c): DNA sequence able to form a hairpin loop – Incorrect

Hairpin loops can form whenever there are inverted repeats or complementary sequences within a single strand, and they are common non‑coding secondary structures in both DNA and RNA across the genome. While such structures can influence gene expression or genome stability, their presence is not specific to genes, because many intergenic, intronic, and regulatory regions can also form hairpins.​

Therefore, the mere ability of a DNA segment to form a hairpin loop does not uniquely identify it as a gene; it only indicates structural potential, not coding capacity or expression.​

Option (d): Multiple short repeats – Incorrect

Short tandem repeats (STRs) or other simple repeats are abundant throughout genomes and are found in promoters, introns, intergenic regions, and even non-functional DNA. Although some repeats in promoters or regulatory regions can modulate gene expression, repeats themselves are not a hallmark of genes and occur in many non-gene contexts.​

Because short repeats have diverse functions and locations, their presence alone cannot be used to say that a DNA segment is a gene; they lack the direct link to transcription that EST evidence provides.​

Summary Table: Which Feature Best Indicates a Gene?

Thus, option (a) multiple expressed sequence tags (ESTs) of the DNA sequence is the correct choice, because it directly reflects expression of that genomic region as RNA, which is the defining property of a gene.​