REXO1

Summary

REXO1 (RNA exonuclease 1 homolog, HGNC:24616) is a protein-coding gene on chromosome 19p13.3, encoding RNA exonuclease 1 homolog (Q8N1G1). Seems to have no detectable effect on transcription elongation in vitro.

Predicted to enable exonuclease activity. Predicted to be involved in rRNA 3’-end processing. Located in nuclear body.

Source: NCBI Gene 57455 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 284 total
• MANE Select transcript: NM_020695

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24616
Approved symbol	REXO1
Name	RNA exonuclease 1 homolog
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	EloA-BP1, KIAA1138
Ensembl gene	ENSG00000079313
Ensembl biotype	protein_coding
OMIM	609614
Entrez	57455

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000170168, ENST00000586291, ENST00000586343, ENST00000587404, ENST00000587524, ENST00000588743, ENST00000590936, ENST00000643515, ENST00000919437, ENST00000919438, ENST00000919439

RefSeq mRNA: 1 — MANE Select: NM_020695 NM_020695

CCDS: CCDS32866

Canonical transcript exons

ENST00000170168 — 16 exons

Exon	Start	End
ENSE00000655704	1816225	1816345
ENSE00000655711	1817219	1817329
ENSE00000892148	1815248	1816154
ENSE00000892149	1816431	1816569
ENSE00001633860	1823572	1823785
ENSE00001665814	1825839	1825943
ENSE00001684128	1821519	1821682
ENSE00001752596	1819934	1820057
ENSE00002300170	1848202	1848483
ENSE00002711113	1826878	1828631
ENSE00003513973	1818706	1818843
ENSE00003583964	1819018	1819131
ENSE00003657801	1816698	1816813
ENSE00003723483	1818482	1818595
ENSE00003747059	1820264	1820395
ENSE00003747349	1817707	1817780

Expression profiles

Bgee: expression breadth ubiquitous, 173 present calls, max score 97.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2967 / max 193.3725, expressed in 1757 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178074	7.6518	1749
178075	0.6024	312
178070	0.0273	3
178069	0.0076	3
178068	0.0050	3
178071	0.0025	2

Top tissues by expression

228 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	97.78	gold quality
left testis	UBERON:0004533	97.63	gold quality
right adrenal gland cortex	UBERON:0035827	95.64	gold quality
right adrenal gland	UBERON:0001233	95.35	gold quality
left adrenal gland cortex	UBERON:0035825	94.84	gold quality
left adrenal gland	UBERON:0001234	94.80	gold quality
testis	UBERON:0000473	94.04	gold quality
adrenal cortex	UBERON:0001235	93.36	gold quality
spleen	UBERON:0002106	93.19	gold quality
mucosa of transverse colon	UBERON:0004991	93.08	gold quality
skin of leg	UBERON:0001511	92.81	gold quality
sural nerve	UBERON:0015488	92.58	gold quality
granulocyte	CL:0000094	92.47	gold quality
adrenal gland	UBERON:0002369	92.36	gold quality
right frontal lobe	UBERON:0002810	92.33	gold quality
skin of abdomen	UBERON:0001416	92.24	gold quality
apex of heart	UBERON:0002098	91.77	gold quality
right lobe of liver	UBERON:0001114	91.71	gold quality
lower esophagus mucosa	UBERON:0035834	91.47	gold quality
transverse colon	UBERON:0001157	91.45	gold quality
right hemisphere of cerebellum	UBERON:0014890	91.38	gold quality
left uterine tube	UBERON:0001303	91.22	gold quality
right lung	UBERON:0002167	91.13	gold quality
small intestine Peyer’s patch	UBERON:0003454	91.03	gold quality
putamen	UBERON:0001874	90.90	gold quality
upper lobe of left lung	UBERON:0008952	90.77	gold quality
right ovary	UBERON:0002118	90.70	gold quality
anterior cingulate cortex	UBERON:0009835	90.64	gold quality
left ovary	UBERON:0002119	90.51	gold quality
cerebellar hemisphere	UBERON:0002245	90.51	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting REXO1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-4489	99.50	65.56	785
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-371A-5P	99.08	66.51	1914
HSA-MIR-5001-5P	99.05	66.76	1972

Literature-anchored findings (GeneRIF, showing 3)

• cloning and characterization of a novel human exonuclease domain-containing protein, Elongin A-binding protein 1; it is capable of binding not only the NH(2)-terminal approximately 120 amino acid region of Elongin A, but also that of SII (PMID:12943681)
• These findings showed that REX1 regulates the proliferation/differentiation of human mesenchymal stem cells through the suppression of p38 MAPK signaling via the direct suppression of MKK3. (PMID:20463961)
• Loss of REX1 expression demarcates stable, OCT4-positive lineage pluripotent human embryonic stem cells. (PMID:23437358)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rexo1	ENSMUSG00000047417
rattus_norvegicus	Rexo1	ENSRNOG00000017916

Paralogs (5): REXO5 (ENSG00000005189), ISG20L2 (ENSG00000143319), REXO4 (ENSG00000148300), ISG20 (ENSG00000172183), AEN (ENSG00000181026)

Protein

Protein identifiers

RNA exonuclease 1 homolog — Q8N1G1 (reviewed: Q8N1G1)

Alternative names: Elongin-A-binding protein 1, Transcription elongation factor B polypeptide 3-binding protein 1

All UniProt accessions (4): Q8N1G1, A0A087WY50, A0A2R8Y7I5, K7ESH4

UniProt curated annotations — full annotation on UniProt →

Function. Seems to have no detectable effect on transcription elongation in vitro.

Subunit / interactions. Interacts with TCEA2 and ELOA.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the REXO1/REXO3 family.

RefSeq proteins (1): NP_065746* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012337	RNaseH-like_sf	Homologous_superfamily
IPR013520	Ribonucl_H	Domain
IPR031736	REXO1-like_dom	Domain
IPR034922	REX1-like_exo	Domain
IPR036397	RNaseH_sf	Homologous_superfamily
IPR047021	REXO1/3/4-like	Family

Pfam: PF15870

UniProt features (28 total): modified residue 9, compositionally biased region 6, region of interest 5, sequence variant 4, chain 1, domain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N1G1-F1	59.13	0.20

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (9): 191, 287, 289, 358, 459, 499, 526, 610, 914

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOMF_NUCLEASE_ACTIVITY, YY1_Q6, YY1_02, GOBP_RRNA_3_END_PROCESSING, CONRAD_STEM_CELL, GOMF_EXONUCLEASE_ACTIVITY, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GATGKMRGCG_UNKNOWN, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, GCCATNTTG_YY1_Q6, GOCC_NUCLEAR_BODY, chr19p13, AAGWWRNYGGC_UNKNOWN, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS

GO Biological Process (1): rRNA 3’-end processing (GO:0031125)

GO Molecular Function (4): nucleic acid binding (GO:0003676), exonuclease activity (GO:0004527), nuclease activity (GO:0004518), hydrolase activity (GO:0016787)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear body (GO:0016604)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
rRNA processing	1
RNA 3’-end processing	1
binding	1
nuclease activity	1
hydrolase activity, acting on ester bonds	1
catalytic activity, acting on a nucleic acid	1
catalytic activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nucleoplasm	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1568 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
REXO1	ELOA	Q14241	918
REXO1	TCEA1	P23193	739
REXO1	ELOA2	Q8IYF1	693
REXO1	POLR2A	P24928	553
REXO1	EML3	Q32P44	430
REXO1	REXO2	Q9Y3B8	426
REXO1	DDX51	Q8N8A6	409
REXO1	SCAMP4	Q969E2	401
REXO1	SKIC8	Q9GZS3	401
REXO1	ZNF276	Q8N554	400
REXO1	C19orf25	Q9UFG5	396
REXO1	DUS3L	Q96G46	384
REXO1	LEO1	Q8WVC0	383
REXO1	VPS9D1	Q9Y2B5	379
REXO1	PPIE	Q9UNP9	371

IntAct

10 interactions, top by confidence:

A	B	Type	Score
REXO1	H3-4	psi-mi:“MI:0915”(physical association)	0.400
REXO1	UBA52	psi-mi:“MI:0915”(physical association)	0.400
DGCR6	REXO1	psi-mi:“MI:0915”(physical association)	0.400
Rprd1b	POLR2B	psi-mi:“MI:0914”(association)	0.350
AP2M1	C1orf226	psi-mi:“MI:0914”(association)	0.350
SSRP1	DDX39A	psi-mi:“MI:0914”(association)	0.350
SMNDC1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
PAFAH1B2	REXO1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (22): REXO1 (Affinity Capture-MS), TCEB3 (Affinity Capture-Western), TCEB3 (Reconstituted Complex), REXO1 (Two-hybrid), REXO1 (Affinity Capture-MS), REXO1 (Affinity Capture-MS), REXO1 (Affinity Capture-MS), REXO1 (Affinity Capture-MS), REXO1 (Two-hybrid), REXO1 (Proximity Label-MS), REXO1 (Proximity Label-MS), REXO1 (Affinity Capture-MS), REXO1 (Affinity Capture-MS), REXO1 (Affinity Capture-MS), REXO1 (Affinity Capture-MS)

ESM2 similar proteins: A2A7S8, A5D7K1, A5PK23, B1AXH1, F1QGH6, O94885, O95402, Q08495, Q08DM1, Q3T044, Q499V8, Q5HYW2, Q5PQP4, Q5R4B6, Q5R8Q8, Q5SYE7, Q5T0Z8, Q5U2R6, Q6PDH0, Q6PFX7, Q6PGN9, Q6ZVC0, Q7TT28, Q80U35, Q80VC9, Q80Z38, Q86UU1, Q86WR7, Q8BI29, Q8C5R2, Q8CAF4, Q8JZX9, Q8K4J6, Q8N1G1, Q8TF72, Q91Z58, Q969V6, Q96A73, Q9BW04, Q9D0P7

Diamond homologs: A1A5R7, A1Z7K9, A3KPE8, A3LRV8, A4RF51, A5DAD0, A5E1W0, B2GUW6, G0SAK8, O94375, O94443, P0C581, P0CQ08, P0CQ09, P0CQ44, P0CQ45, P48778, P53010, P53015, P53331, Q08237, Q09798, Q0CJU7, Q10124, Q2GSV2, Q2T9U5, Q2YDK1, Q3U1G5, Q4PER6, Q4R9F7, Q4WYA1, Q504Q3, Q54U94, Q5AL29, Q5APK0, Q5B367, Q5F450, Q5REE2, Q6AXU3, Q6C462

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

284 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	243
Likely benign	17
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3516 predictions. Top by Δscore:

Variant	Effect	Δscore
19:1816453:T:A	donor_gain	1.0000
19:1816694:ACAC:A	donor_loss	1.0000
19:1816697:C:CG	donor_loss	1.0000
19:1816809:TAGGA:T	acceptor_gain	1.0000
19:1816810:AGGA:A	acceptor_gain	1.0000
19:1816811:GGA:G	acceptor_gain	1.0000
19:1816812:GA:G	acceptor_gain	1.0000
19:1816814:C:CC	acceptor_gain	1.0000
19:1816814:CTGC:C	acceptor_loss	1.0000
19:1816815:T:G	acceptor_loss	1.0000
19:1816817:C:CT	acceptor_gain	1.0000
19:1816818:G:T	acceptor_gain	1.0000
19:1817214:CTCA:C	donor_loss	1.0000
19:1817215:TCACC:T	donor_loss	1.0000
19:1817216:CACC:C	donor_loss	1.0000
19:1817217:A:AC	donor_gain	1.0000
19:1817217:A:T	donor_loss	1.0000
19:1817218:C:CC	donor_gain	1.0000
19:1817218:C:CG	donor_loss	1.0000
19:1817218:CCAT:C	donor_gain	1.0000
19:1817325:TGTTG:T	acceptor_gain	1.0000
19:1817326:GTTG:G	acceptor_gain	1.0000
19:1817327:T:C	acceptor_gain	1.0000
19:1817327:TTG:T	acceptor_gain	1.0000
19:1817328:TG:T	acceptor_gain	1.0000
19:1817330:C:CA	acceptor_loss	1.0000
19:1817330:C:CC	acceptor_gain	1.0000
19:1817336:G:C	acceptor_gain	1.0000
19:1817336:G:GC	acceptor_gain	1.0000
19:1817702:CTCA:C	donor_loss	1.0000

AlphaMissense

7855 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:1816109:A:G	L1208P	1.000
19:1816109:A:T	L1208Q	1.000
19:1816117:G:C	C1205W	1.000
19:1816118:C:T	C1205Y	1.000
19:1816263:A:G	L1180P	1.000
19:1816308:A:G	F1165S	1.000
19:1816324:C:G	D1160H	1.000
19:1816444:A:G	L1148P	1.000
19:1816463:G:C	H1142D	1.000
19:1816465:C:A	G1141V	1.000
19:1816465:C:T	G1141E	1.000
19:1816466:C:G	G1141R	1.000
19:1816466:C:T	G1141R	1.000
19:1816471:A:T	L1139H	1.000
19:1816566:A:C	F1107L	1.000
19:1816566:A:T	F1107L	1.000
19:1816568:A:G	F1107L	1.000
19:1817225:G:C	C1065W	1.000
19:1819993:G:T	A864D	1.000
19:1820325:A:G	L822P	1.000
19:1820338:G:T	R818S	1.000
19:1816119:A:G	C1205R	0.999
19:1816127:G:T	A1202D	0.999
19:1816128:C:G	A1202P	0.999
19:1816129:G:C	D1201E	0.999
19:1816129:G:T	D1201E	0.999
19:1816130:T:C	D1201G	0.999
19:1816130:T:G	D1201A	0.999
19:1816131:C:G	D1201H	0.999
19:1816139:G:A	S1198F	0.999

dbSNP variants (sampled 300 via entrez): RS1000110872 (19:1843433 G>A,C,T), RS1000140903 (19:1850149 T>C), RS1000372648 (19:1829621 C>A,T), RS1000417486 (19:1849884 G>A,T), RS1000444525 (19:1838163 T>A), RS1000507651 (19:1841724 C>A,T), RS1000537001 (19:1841494 G>A), RS1000540379 (19:1841337 C>G,T), RS1000609783 (19:1820176 T>C,G), RS1000655468 (19:1818330 GC>G), RS1000722711 (19:1837295 C>A), RS1000777255 (19:1841307 C>T), RS1000807287 (19:1845309 C>T), RS1000843656 (19:1832793 G>A), RS1000946179 (19:1832515 C>G,T)

Disease associations

OMIM: gene MIM:609614 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST008129_31	Body mass index	2.000000e-11
GCST010774_10	Essential hypertension (time to event)	4.000000e-08
GCST90002396_6	Mean reticulocyte volume	1.000000e-18
GCST90002397_396	Mean spheric corpuscular volume	7.000000e-24

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004918	age at diagnosis
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	2
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
dicrotophos	increases expression	1
bufotalin	increases expression	1
triphenyl phosphate	affects expression	1
benzo(e)pyrene	increases methylation	1
cupric chloride	increases expression	1
beta-methylcholine	affects expression	1
fipronil	decreases expression	1
abrine	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Atrazine	increases expression	1
Caffeine	increases phosphorylation	1
Doxorubicin	decreases expression	1
Methapyrilene	increases methylation	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Dronabinol	increases expression	1
Thiram	increases expression	1
Urethane	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1
p-Chloromercuribenzoic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.