PRDM1, human gene | AUM BioTech

01 Summary and function

What PRDM1 does

This gene encodes a protein that acts as a repressor of beta-interferon gene…

NCBI Gene summary

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Gene summary

This gene encodes a protein that acts as a repressor of beta-interferon gene expression. The protein binds specifically to the PRDI (positive regulatory domain I element) of the beta-IFN gene promoter. Transcription of this gene increases upon virus induction. Two alternatively spliced transcript variants that encode different isoforms have been reported.

Provided by RefSeq, Jul 2008, through NCBI Gene. NCBI disclaimer

Protein function

PR domain zinc finger protein 1, O75626

Transcription factor that mediates a transcriptional program in various innate and adaptive immune tissue-resident lymphocyte T cell types such as tissue-resident memory T (Trm), natural killer (trNK) and natural killer T (NKT) cells and negatively regulates gene expression of proteins that promote the egress of tissue-resident T-cell populations from non-lymphoid organs. Plays a role in the development, retention and long-term establishment of adaptive and innate tissue-resident lymphocyte T cell types in non-lymphoid organs, such as the skin and gut, but also in other nonbarrier tissues like liver and kidney, and therefore may provide immediate immunological protection against reactivating infections or viral reinfection (By similarity). Binds specifically to the PRDI element in the promoter of the beta-interferon gene (PubMed:1851123). Drives the maturation of B-lymphocytes into Ig secreting cells (PubMed:12626569). Associates with the transcriptional repressor ZNF683 to chromatin at gene promoter regions (By similarity). Binds to the promoter and acts as a transcriptional repressor of IRF8, thereby promotes transcription of osteoclast differentiation factors such as NFATC1 and EEIG1 (By similarity)

NCBI Gene summary · NCBI Gene annotation RS_2025_08 · read 2026-09-29 ET · NCBI Gene 639Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
UniProtKB function · 2026_03 · read 2026-09-29 ET · UniProt O75626UniProt data are available under the Creative Commons Attribution 4.0 licence.

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02 Transcripts and isoforms

The RNA a design targets

9 RefSeq and 13 Ensembl transcripts on GRCh38.p14; MANE Select NM_001198.4.

NCBI Datasets · Ensembl

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What this tells you

A gene is silenced through its RNA, so the transcript is the target, not the gene. The map draws the isoforms 5' to 3', with the coding sequence taller than the untranslated regions and the isoforms aligned on the genome, so an exon they share sits in one column. A gene with many isoforms, or whose isoforms carry thousands of exons, draws the reference ones first and says how many it is holding back; the rest are drawn when you ask for them.

A sequence in a region every isoform carries knocks the whole gene down; one in an exon only some isoforms carry is isoform-specific. The MANE Select transcript in human, or the RefSeq Select and Ensembl canonical transcripts in mouse and rat, is the usual reference for a design. Where the two catalogues disagree, both are shown and neither is preferred.

Placed on GRCh38.p14 (GCF_000001405.40). MANE Select marks the one transcript RefSeq and Ensembl agree is the reference for this gene.

RefSeq 9 transcripts

coding sequence, tall
untranslated region, thin
non-coding exon
intron, fixed width

Genomic strand: plus. Drawn 5' to 3', so exon 1 sits at the left here and at the lowest coordinate on the chromosome.

MANE Select

Drawn 5' to 3' from each transcript's exons as placed on the reference assembly; exon 1 is the 5' exon on the transcript's own strand. Exon blocks are to scale with each other; introns are drawn at one fixed width whatever their length, so the map is not to scale along the chromosome. Numbers are exon ranks along the strand; a rank is omitted where the exon is too narrow to carry it.

A window on one transcript

One pixel of the map above stands for several bases, and a block too short to see is drawn wider than its own scale, so the map chooses a region and the sequence here chooses the window. Click an exon on a row of the map, or drag across a row; then set the exact start and end below.

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Transcript

No transcript is chosen.

Once a window is chosen this panel shows its length, its G and C count as a percentage of that length, the letters it is made of, the exons it falls in, whether it crosses a junction, and its antisense strand.

RefSeq transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_001198.4matches ENST00000369096.9	transcript variant 1	protein coding	MANE Select	7	5,148 nt	825 aaNP_001189.2	Ready in a moment
XM_047419246.1matches ENST00000652320.1	transcript variant X4	protein coding model	none	8	5,179 nt	789 aaXP_047275202.1	Ready in a moment
XM_011536062.4matches ENST00000648754.2	transcript variant X1	protein coding model	none	7	5,065 nt	839 aaXP_011534364.1	Ready in a moment
XM_047419247.1	Ready in a moment

Not listed, because the source places them on another assembly only: XM_054356206.1 (not placed on GRCh38.p14); XM_054356207.1 (not placed on GRCh38.p14); XM_054356208.1 (not placed on GRCh38.p14); XM_054356209.1 (not placed on GRCh38.p14); XM_054356210.1 (not placed on GRCh38.p14); XM_054356211.1 (not placed on GRCh38.p14); XM_054356212.1 (not placed on GRCh38.p14).

NCBI Datasets, RefSeq transcripts · NCBI Datasets 18.38.0; GCF_000001405.40-RS_2025_08 · read 2026-09-29 ET · NCBI Gene 639Data from NCBI, provided as is; NCBI's policies and disclaimers apply.

Ensembl 13 transcripts

A window on one transcript

One pixel of the map above stands for several bases, and a block too short to see is drawn wider than its own scale, so the map chooses a region and the sequence here chooses the window. Click an exon on a row of the map, or drag across a row; then set the exact start and end below.

These controls are ready in a moment.

Transcript

No transcript is chosen.

Once a window is chosen this panel shows its length, its G and C count as a percentage of that length, the letters it is made of, the exons it falls in, whether it crosses a junction, and its antisense strand.

Lengths are spliced lengths, as each source states them. Exon ranks follow the strand: on a minus-strand gene exon 1 has the highest genomic coordinate. Reference assembly for human: GRCh38.

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03 Expression by tissue

Where PRDM1 is expressed

54 GTEx tissues; the highest median in Esophagus - Mucosa, 40.1 TPM.

GTEx

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04 Protein

The protein PRDM1 encodes

825 residues, reviewed O75626; 16 entries from the member databases this page shows along the chain; mean pLDDT 55.59; 3 PDB entries.

UniProt · InterPro · AlphaFold DB · PDBe

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05 Interactions

Proteins STRING associates with PRDM1

The 25 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; STAT3, IRF4, EHMT2 lead.

STRING v12.0

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06 Pathways

Where PRDM1 acts, as Reactome curates it

3 curated, 0 inferred Reactome pathways for O75626 in human, v97.

Reactome

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07 Disease associations

Diseases linked to PRDM1

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08 Variants

Classified variants of PRDM1

ClinVar asked this site to slow down, so the variant counts could not be read. Try again in a minute. Reference bd617c47-641.

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09 Constraint

How much variation PRDM1 tolerates

pLI above 0.9999 and LOEUF 0.329 in gnomAD v4 (GRCh38), on ENST00000369096.9.

gnomAD

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10 Orthologs

The same gene in mouse, rat and human

Mouse Prdm1 by 3 of 3 votes; rat Prdm1 by 3 of 3 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference c502a6e3-5d0.

Alliance · NCBI · Ensembl Compara

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11 MicroRNAs

MicroRNAs hosted within PRDM1

No annotated microRNA lies within PRDM1 in Ensembl release 116, on GRCh38.p14.

Ensembl · miRBase

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12 Long non-coding RNAs

Long non-coding RNAs at the PRDM1 locus

3 long non-coding RNA genes overlap PRDM1 in Ensembl release 116, 2 antisense, none with a symbol.

Ensembl

Order against a long non-coding RNA

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13 Literature

Papers that mention PRDM1

8,645 PubMed-indexed papers mention PRDM1 at Europe PMC, newest first. Europe PMC ignores letter case, so the count also covers another species' symbol spelled with the same letters.

Europe PMC

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Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000369096.9matches NM_001198.4	PRDM1-203	protein coding	MANE SelectEnsembl canonical	7	5,148 nt	825 aaENSP00000358092.4	Ready in a moment
ENST00001135189.1	PRDM1-213	protein coding	none	7	5,295 nt	825 aaENSP00000809507.1	Ready in a moment
ENST00000648754.2	PRDM1-208	protein coding	none	7	5,233 nt	839 aaENSP00000498029.1	Ready in a moment
ENST00000967211.2	PRDM1-211	protein coding	none	6	5,166 nt	782 aaENSP00000637270.1	Ready in a moment
ENST00000651185.1	PRDM1-209	protein coding	none	7	5,070 nt	789 aaENSP00000498716.1	Ready in a moment
ENST00000652320.1	PRDM1-210	protein coding	none	7	5,066 nt	789 aaENSP00000498580.1	Ready in a moment
ENST00000369091.7	PRDM1-202	protein coding	none	7	5,043 nt	789 aaENSP00000358087.2	Ready in a moment
ENST00000369089.3	PRDM1-201	protein coding	none	5	4,675 nt	691 aaENSP00000358085.3	Ready in a moment
ENST00001106368.1	PRDM1-212	protein coding	none	2	4,353 nt	118 aaENSP00000776173.1	Ready in a moment
ENST00000424894.1	PRDM1-204	protein coding	none	3	583 nt	63 aaENSP00000395566.1	Ready in a moment
ENST00000450060.5	PRDM1-205	protein coding	none	3	583 nt	171 aaENSP00000399772.1	Ready in a moment
ENST00000489365.1	PRDM1-207	retained intron	none	2	649 nt	none	Ready in a moment
ENST00000481163.1	PRDM1-206	retained intron	none	2	580 nt	none	Ready in a moment

PRDM1

PRDM1

What PRDM1 does

The RNA a design targets

Where PRDM1 is expressed

The protein PRDM1 encodes

Proteins STRING associates with PRDM1

Where PRDM1 acts, as Reactome curates it

Diseases linked to PRDM1

Classified variants of PRDM1

How much variation PRDM1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within PRDM1

Long non-coding RNAs at the PRDM1 locus

Papers that mention PRDM1

PRDM1

What PRDM1 does

Gene summary

Protein function

The RNA a design targets

RefSeq 9 transcripts

A window on one transcript

Ensembl 13 transcripts

A window on one transcript

Where PRDM1 is expressed

The protein PRDM1 encodes

Proteins STRING associates with PRDM1

Where PRDM1 acts, as Reactome curates it

Diseases linked to PRDM1

Classified variants of PRDM1

How much variation PRDM1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within PRDM1

Long non-coding RNAs at the PRDM1 locus

Papers that mention PRDM1

From PRDM1 to a sequence that silences it

Choose the region

Cover the isoforms you mean

Think across species early

Check expression in your model

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Gene summary

Protein function

RefSeq 9 transcripts

A window on one transcript

Ensembl 13 transcripts

A window on one transcript