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Gene, transcript and protein: connecting the records

In brief

A molecular story can be represented by several records. A gene is described on a genomic sequence; a transcript represents an RNA product; a protein record describes an amino-acid sequence. RefSeq holds genomic, transcript and protein sequences as distinct connected objects. Begin by identifying which object you have opened. [1]

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Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.
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For a protein-coding eukaryotic gene, compare the transcripts and their exons. Mature RNA can contain untranslated regions, whereas CDS identifies the coding portion. Its entire length therefore need not be three times the protein length. Check the protein linked to the selected transcript. NCBI provides these links, but does not create separate prokaryotic RefSeq transcript records in the same way.

[2]
Evidence for this statement

Source-based explanation

Where to check this statement

guide-source-2
Official guidance on linked transcripts. Separate RefSeq transcript records are not assumed for all prokaryotes.

A symbol such as BRCA2 is convenient for reading. Reproducible comparisons also need the organism, identifier, version and assembly. A sequence accession identifies a record; its version suffix specifies the sequence version. Coordinates belong to an assembly. A matching gene name alone is not enough to transfer a selected region between assemblies.

[3]
Evidence for this statement

Source-based explanation

Where to check this statement

guide-source-3
Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.

Annotation provenance matters too. In RefSeq, XM_/XP_ identify model records and differ from NM_/NP_. These labels describe the record's origin rather than a simple “correct” or “incorrect” verdict. A transcript update need not change its protein sequence, so the two version numbers can differ.

[4]
Evidence for this statement

Source-based explanation

Where to check this statement

guide-source-4
Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.

Try the route

Try it. In BRCA2, choose an available transcript, locate its CDS and open the linked protein. Save the selected identifiers, assembly version and region. Repeat the reading with FLC. Then open DnaA and check the strain designation: K-12 and MG1655 must not be silently substituted. If a separate transcript record is not provided, record that as a state of the available data.

Evidence for this statement

EcoGenesis learning activity

    Check exact identity

    Check your understanding. A matching symbol does not prove sequence identity. Different protein lengths first call for checking isoform, coverage and record identity before suggesting a biological explanation.

    Evidence for this statement

    EcoGenesis learning activity

      From gene to protein

      Possible record relationships for a protein-coding eukaryotic gene. The source determines the actual transcripts and products of the selected gene.

      Evidence for this statement

      EcoGenesis learning activity

        Teaching diagram · open a label to read its explanation
        1. Genomic locus

          First preserve the assembly, sequence version and coordinates. Below are two illustrative protein-coding transcripts from one locus: a reading example, not an annotation of a particular gene.

        1. RNA A: UTR · CDS · UTR

          UTRs belong to the transcript but lie outside its protein-coding CDS. Find the transcript accession, version and CDS relationship in the source record. No lengths are shown here.

        2. RNA B: UTR · CDS · UTR

          A second transcript needs its own record. A gene symbol alone does not establish its existence or a different product: read the actual variants and relationships in the selected annotation.

        1. Product A

          Follow an explicit protein-sequence link and retain its accession/version. The protein name alone does not identify the selected transcript.

        2. Product B

          Check whether the source distinguishes this product from A. Two transcripts do not necessarily produce different amino-acid sequences.

        • Genomic locus → RNA A: UTR · CDS · UTR: Illustrative variant A
        • Genomic locus → RNA B: UTR · CDS · UTR: Illustrative variant B
        • RNA A: UTR · CDS · UTR → Product A: CDS product; verify the record link
        • RNA B: UTR · CDS · UTR → Product B: CDS product; verify the record link

        Worked result: keep separate rows

        A completed teaching note can have a gene row G, transcript rows T1 and T2, and protein rows P1 and P2. The arrows describe the mappings supplied in the example. Two transcript rows are not two genes, and a matching label is not a confirmed mapping. In a real comparison, add assembly, accession and version to the appropriate row; leave a missing correspondence explicitly unresolved.

        Evidence for this statement

        EcoGenesis

          Continue with an organism

          The photographs and molecular record come from separate source materials.

          Norway spruce →Arabidopsis thaliana →

          Your research question

          Save the article to return to your question and this source version.

          Plan a test

          This is your research plan. Completing these fields does not confirm a hypothesis.

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          Sources and versions

          Editorial draft · human review pending

          1. NCBI RefSeq

            2026-09-19 · Terms of use on source site

            Provenance and original
            Source version
            Page checked 19 September 2026; no immutable provider release asserted
            Source reading scope
            Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.
            Location in the original source
            Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.
          2. Moving from NCBI Gene to RNA and protein

            2026-09-19 · Terms of use on source site

            Provenance and original
            Source version
            Page checked 19 September 2026; no immutable provider release asserted
            Source reading scope
            Official guidance on linked transcripts. Separate RefSeq transcript records are not assumed for all prokaryotes.
            Location in the original source
            Official guidance on linked transcripts. Separate RefSeq transcript records are not assumed for all prokaryotes.
          3. Understanding GenBank record fields

            2026-09-19 · Terms of use on source site

            Provenance and original
            Source version
            Page checked 19 September 2026; no immutable provider release asserted
            Source reading scope
            Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.
            Location in the original source
            Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.
          4. RefSeq explanations

            2026-09-19 · Terms of use on source site

            Provenance and original
            Source version
            Page checked 19 September 2026; no immutable provider release asserted
            Source reading scope
            Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.
            Location in the original source
            Official record-type, accession/version and linked-transcript descriptions; dynamic database totals are not included.
          Inspect structured data
          Content version
          5943f63b30ed3c0b89dc7940beda2fcfdebe5d903605de032c1d36180d44a566
          Source version
          guides-20260919@cd1e4a0a6f0c71995fb6e076b59bd2ee930c2104150357fab50fc56f5f6e80fe
          Updated
          2026-10-01