REX1BD

Summary

REX1BD (required for excision 1-B domain containing, HGNC:26098) is a protein-coding gene on chromosome 19p13.11, encoding Required for excision 1-B domain-containing protein (Q96EN9).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001100418

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26098
Approved symbol	REX1BD
Name	required for excision 1-B domain containing
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20850, FLJ30108, FLJ34606, FLJ37391
Ensembl gene	ENSG00000006015
Ensembl biotype	protein_coding
Entrez	55049

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000358607, ENST00000450195, ENST00000595077, ENST00000595490, ENST00000597371, ENST00000598375, ENST00000600997, ENST00000601736, ENST00000870231, ENST00000870232, ENST00000870233, ENST00000870234, ENST00000870235, ENST00000925923, ENST00000950225

RefSeq mRNA: 2 — MANE Select: NM_001100418 NM_001100418, NM_001100419

CCDS: CCDS42524, CCDS46019

Canonical transcript exons

ENST00000358607 — 5 exons

Exon	Start	End
ENSE00000691132	18588995	18589077
ENSE00001432086	18589413	18589683
ENSE00003098508	18588798	18588900
ENSE00003671015	18590854	18590933
ENSE00003906391	18592108	18592337

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 97.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.3771 / max 288.7617, expressed in 1824 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174699	24.3253	1820
174700	3.6521	1559
174701	0.3997	193

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	97.88	gold quality
tendon of biceps brachii	UBERON:0008188	97.37	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.32	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.02	gold quality
granulocyte	CL:0000094	96.82	gold quality
right frontal lobe	UBERON:0002810	96.72	gold quality
cerebellar hemisphere	UBERON:0002245	96.68	gold quality
cerebellar cortex	UBERON:0002129	96.62	gold quality
anterior cingulate cortex	UBERON:0009835	96.62	gold quality
cingulate cortex	UBERON:0003027	96.53	gold quality
mucosa of transverse colon	UBERON:0004991	96.46	gold quality
gastrocnemius	UBERON:0001388	96.16	gold quality
right atrium auricular region	UBERON:0006631	95.88	gold quality
nucleus accumbens	UBERON:0001882	95.87	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	95.87	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.78	gold quality
endocervix	UBERON:0000458	95.76	gold quality
amygdala	UBERON:0001876	95.69	gold quality
cerebellum	UBERON:0002037	95.53	gold quality
muscle of leg	UBERON:0001383	95.44	gold quality
right lobe of liver	UBERON:0001114	95.34	gold quality
left coronary artery	UBERON:0001626	95.28	gold quality
caudate nucleus	UBERON:0001873	95.09	gold quality
prefrontal cortex	UBERON:0000451	95.03	gold quality
right uterine tube	UBERON:0001302	95.02	gold quality
right ovary	UBERON:0002118	95.00	gold quality
coronary artery	UBERON:0001621	94.96	gold quality
spleen	UBERON:0002106	94.96	gold quality
body of uterus	UBERON:0009853	94.95	gold quality
putamen	UBERON:0001874	94.93	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ENAD-17	no	520.43
E-HCAD-13	no	2.92
E-HCAD-5	no	2.18
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• A human protein of unknown function FLJ20850 interacted specifically with deletion mutant hepatitis B core proteins. (PMID:19770013)
• Heterochromatin repeat organization at an individual level: Rex1BD and the 14-3-3 protein coordinate to shape the epigenetic landscape within heterochromatin repeats. (PMID:38679759)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rex1bd	ENSMUSG00000058833
rattus_norvegicus	Rex1bd	ENSRNOG00000019990

Protein

Protein identifiers

Required for excision 1-B domain-containing protein — Q96EN9 (reviewed: Q96EN9)

All UniProt accessions (3): Q96EN9, M0QYI9, M0R0T3

Isoforms (3)

UniProt ID	Names	Canonical?
Q96EN9-1	1	yes
Q96EN9-2	2
Q96EN9-3	3

RefSeq proteins (2): NP_001093888, NP_001093889 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039491	REX1-B	Family

Pfam: PF14966

UniProt features (6 total): splice variant 3, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EN9-F1	74.21	0.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 114 (showing top): CATRRAGC_UNKNOWN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, chr19p13, CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN, JIANG_VHL_TARGETS, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN, MARTENS_TRETINOIN_RESPONSE_DN, DELACROIX_RARG_BOUND_MEF, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GCNP_SHH_UP_LATE.V1_DN, GSE10240_CTRL_VS_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_DN, DIDO1_TARGET_GENES, FOXD2_TARGET_GENES, GLI3_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

356 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
REX1BD	CRLF1	O75462	829
REX1BD	TPGS1	Q6ZTW0	625
REX1BD	CLCF1	Q9UBD9	582
REX1BD	PPP1R16A	Q96I34	545
REX1BD	OXLD1	Q5BKU9	441
REX1BD	TRAPPC2L	Q9UL33	433
REX1BD	OR5M11	Q96RB7	419
REX1BD	SDR39U1	Q9NRG7	398
REX1BD	TRIR	Q9BQ61	396
REX1BD	MRPL41	Q8IXM3	392
REX1BD	CNTFR	P26992	386
REX1BD	FAM53C	Q9NYF3	374
REX1BD	APOE	P02649	374
REX1BD	UBALD1	Q8TB05	372
REX1BD	CCDC85B	Q15834	371

IntAct

59 interactions, top by confidence:

A	B	Type	Score
MDFI	REX1BD	psi-mi:“MI:0915”(physical association)	0.760
REX1BD	MDFI	psi-mi:“MI:0915”(physical association)	0.760
PSMD13	PSMD11	psi-mi:“MI:0914”(association)	0.750
PSMD7	PSMD11	psi-mi:“MI:0914”(association)	0.730
PSMD14	PSMD11	psi-mi:“MI:0914”(association)	0.650
PSMD3	PSMD11	psi-mi:“MI:0914”(association)	0.650
GPRASP2	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
MAGEA11	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
MAGEA6	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
CTAG1A	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
DMWD	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
REX1BD	GLE1	psi-mi:“MI:0915”(physical association)	0.560
REX1BD	ICAM5	psi-mi:“MI:0915”(physical association)	0.560
DNALI1	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
KLF11	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
NUP58	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
DNAJB6	REX1BD	psi-mi:“MI:0915”(physical association)	0.560
REX1BD	SPRED1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (24): C19orf60 (Affinity Capture-MS), C19orf60 (Two-hybrid), C19orf60 (Affinity Capture-MS), C19orf60 (Affinity Capture-MS), C19orf60 (Proximity Label-MS), MDFI (Two-hybrid), GPRASP2 (Two-hybrid), CTAG1B (Two-hybrid), MAGEA11 (Two-hybrid), MAGEA6 (Two-hybrid), CTAG1A (Two-hybrid), C19orf60 (Two-hybrid), C19orf60 (Two-hybrid), C19orf60 (Affinity Capture-RNA), C19orf60 (Affinity Capture-MS)

ESM2 similar proteins: A0A140LIT1, A0A1B0GVG4, A0A494C0Y3, A0JNH6, A0JNN8, A1A5D9, A2ARS0, A5A769, A5PJP1, A6NC98, A7YWC8, C9JTQ0, O15049, O35764, O95502, P0C7N4, P0DPE3, P58660, Q0P5D1, Q1HCM0, Q2TAC2, Q3LUD3, Q3LUD4, Q3TMW1, Q3UMT1, Q4QRL3, Q5BLP8, Q5JTB6, Q6QNY0, Q6QZQ4, Q8BP01, Q8C7U1, Q8CHW5, Q8K262, Q8N283, Q8N6Y0, Q8TAT2, Q8TER5, Q8TF21, Q91XV7

Diamond homologs: Q17Q97, Q96EN9, Q9CYZ6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 26 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Regulation of activated PAK-2p34 by proteasome mediated degradation	5	92.8×	2e-08
Regulation of ornithine decarboxylase (ODC)	5	90.6×	2e-08
Vpu mediated degradation of CD4	5	88.5×	2e-08
Autodegradation of the E3 ubiquitin ligase COP1	5	88.5×	2e-08
Ubiquitin-dependent degradation of Cyclin D	5	88.5×	2e-08
Cross-presentation of soluble exogenous antigens (endosomes)	5	84.6×	2e-08
Vif-mediated degradation of APOBEC3G	5	84.6×	2e-08
AUF1 (hnRNP D0) binds and destabilizes mRNA	5	82.8×	2e-08

GO biological processes:

GO term	Partners	Fold	FDR
proteasome-mediated ubiquitin-dependent protein catabolic process	5	11.3×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

812 predictions. Top by Δscore:

Variant	Effect	Δscore
19:18589075:GGA:G	donor_gain	1.0000
19:18589076:GAG:G	donor_gain	1.0000
19:18589078:G:GG	donor_gain	1.0000
19:18589684:G:GG	donor_gain	1.0000
19:18589684:GTGA:G	donor_loss	1.0000
19:18590931:G:GT	donor_gain	1.0000
19:18590934:G:GG	donor_gain	1.0000
19:18588856:G:GT	donor_gain	0.9900
19:18588897:CTGGG:C	donor_loss	0.9900
19:18588899:GG:G	donor_gain	0.9900
19:18588899:GGGTG:G	donor_loss	0.9900
19:18588900:GG:G	donor_gain	0.9900
19:18588900:GGT:G	donor_loss	0.9900
19:18588901:G:GG	donor_gain	0.9900
19:18588901:GT:G	donor_loss	0.9900
19:18588902:T:C	donor_loss	0.9900
19:18589043:GC:G	donor_gain	0.9900
19:18589073:GAGGA:G	donor_gain	0.9900
19:18589074:AGGA:A	donor_gain	0.9900
19:18589074:AGGAG:A	donor_loss	0.9900
19:18589075:GGAG:G	donor_gain	0.9900
19:18589076:GA:G	donor_gain	0.9900
19:18589077:AG:A	donor_loss	0.9900
19:18589079:T:A	donor_loss	0.9900
19:18589080:GA:G	donor_loss	0.9900
19:18589679:GCACG:G	donor_gain	0.9900
19:18589685:T:G	donor_loss	0.9900
19:18590852:AGGT:A	acceptor_gain	0.9900
19:18590853:GGTG:G	acceptor_gain	0.9900
19:18590931:GAA:G	donor_gain	0.9900

AlphaMissense

1277 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:18589561:T:C	F111L	0.994
19:18589563:C:A	F111L	0.994
19:18589563:C:G	F111L	0.994
19:18589562:T:G	F111C	0.987
19:18589562:T:C	F111S	0.986
19:18589665:G:C	E145D	0.985
19:18589665:G:T	E145D	0.985
19:18589656:G:C	Q142H	0.983
19:18589656:G:T	Q142H	0.983
19:18592127:G:C	A185P	0.983
19:18589519:T:C	F97L	0.980
19:18589521:C:A	F97L	0.980
19:18589521:C:G	F97L	0.980
19:18589061:T:C	F56L	0.979
19:18589063:C:A	F56L	0.979
19:18589063:C:G	F56L	0.979
19:18589029:T:C	I45T	0.978
19:18589664:A:T	E145V	0.978
19:18592152:T:C	L193P	0.978
19:18592157:T:C	F195L	0.978
19:18592159:T:A	F195L	0.978
19:18592159:T:G	F195L	0.978
19:18592131:T:A	I186N	0.974
19:18589663:G:A	E145K	0.971
19:18589520:T:G	F97C	0.968
19:18589038:T:C	L48P	0.967
19:18592152:T:A	L193H	0.966
19:18589049:C:A	R52S	0.964
19:18592131:T:G	I186S	0.964
19:18589042:G:C	Q49H	0.963

dbSNP variants (sampled 300 via entrez): RS1000758766 (19:18589973 T>A,C), RS1001735680 (19:18588405 G>C), RS1002154207 (19:18590735 G>A,C), RS1002749473 (19:18592268 G>A,T), RS1002803966 (19:18592616 T>G), RS1003008844 (19:18588083 C>A), RS1003033530 (19:18587716 G>A,T), RS1003493435 (19:18591739 T>C), RS1003816920 (19:18591532 C>G,T), RS1004043498 (19:18591767 G>A,C), RS1004338193 (19:18590772 G>A,T), RS1005088752 (19:18590615 G>A,C,T), RS1005532004 (19:18586901 T>C), RS1005935020 (19:18589675 C>A,G), RS1006491745 (19:18589451 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90000514_28	Gastroesophageal reflux disease	3.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	3
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
bufotalin	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
aflatoxin B2	decreases methylation	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	increases expression, affects cotreatment	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Lactic Acid	increases expression	1
Vitamin K 3	affects expression	1

Clinical trials (associated diseases)

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