RBMXL1

Summary

RBMXL1 (RBMX like 1, HGNC:25073) is a protein-coding gene on chromosome 1p22.2, encoding RNA binding motif protein, X-linked-like-1 (Q96E39). RNA-binding protein which may be involved in pre-mRNA splicing. It is a common-essential gene (DepMap: required in 97.3% of cancer cell lines).

This gene represents a retrogene of RNA binding motif protein, X-linked (RBMX), which is located on chromosome X. While all introns in the coding sequence have been processed out compared to the RBMX locus, the ORF is intact and there is specific evidence for transcription at this location. The preservation of the ORF by purifying selection in all Old World monkeys carrying it suggests that this locus is likely to be functional, possibly during male meiosis when X chromosomal genes are silenced or during haploid stages of spermatogenesis. This gene shares 5’ exon structure with the cysteine conjugate-beta lyase 2 locus on chromosome 1, but the coding sequences are non-overlapping. Alternative splicing results in two transcript variants.

Source: NCBI Gene 494115 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• Cancer dependency (DepMap): dependent in 97.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_001162536

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25073
Approved symbol	RBMXL1
Name	RBMX like 1
Location	1p22.2
Locus type	gene with protein product
Status	Approved
Aliases	KAT3
Ensembl gene	ENSG00000213516
Ensembl biotype	protein_coding
Entrez	494115

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000321792, ENST00000399794, ENST00000413769, ENST00000652648

RefSeq mRNA: 2 — MANE Select: NM_001162536 NM_001162536, NM_019610

CCDS: CCDS716

Canonical transcript exons

ENST00000652648 — 3 exons

Exon	Start	End
ENSE00001262871	88979456	88984066
ENSE00003472249	88988252	88988351
ENSE00003842449	88992585	88992629

Expression profiles

Bgee: expression breadth ubiquitous, 246 present calls, max score 93.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.2058 / max 99.5673, expressed in 1772 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
13125	13.3929	1782
13127	9.2058	1772
13130	0.5038	302

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cauda epididymis	UBERON:0004360	93.96	gold quality
corpus epididymis	UBERON:0004359	93.49	gold quality
caput epididymis	UBERON:0004358	92.84	gold quality
lower lobe of lung	UBERON:0008949	91.12	gold quality
oral cavity	UBERON:0000167	91.10	gold quality
trabecular bone tissue	UBERON:0002483	87.86	gold quality
superficial temporal artery	UBERON:0001614	87.51	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.49	gold quality
mucosa of paranasal sinus	UBERON:0005030	86.43	gold quality
skin of hip	UBERON:0001554	85.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.51	gold quality
mammalian vulva	UBERON:0000997	85.37	gold quality
cartilage tissue	UBERON:0002418	85.33	gold quality
epithelium of nasopharynx	UBERON:0001951	85.16	gold quality
cortical plate	UBERON:0005343	85.16	gold quality
pigmented layer of retina	UBERON:0001782	84.55	gold quality
jejunal mucosa	UBERON:0000399	84.47	gold quality
ventricular zone	UBERON:0003053	83.88	gold quality
ganglionic eminence	UBERON:0004023	83.76	gold quality
mammary duct	UBERON:0001765	83.55	gold quality
calcaneal tendon	UBERON:0003701	83.50	gold quality
oviduct epithelium	UBERON:0004804	83.46	gold quality
epithelium of mammary gland	UBERON:0003244	83.32	gold quality
trigeminal ganglion	UBERON:0001675	83.29	gold quality
bone marrow	UBERON:0002371	83.19	gold quality
corpus callosum	UBERON:0002336	83.03	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	82.87	gold quality
upper leg skin	UBERON:0004262	82.84	gold quality
ileal mucosa	UBERON:0000331	82.82	gold quality
penis	UBERON:0000989	82.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting RBMXL1, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4799-5P	99.82	70.60	2663

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 97.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

• Transcriptional control of CBX5 by the RNA binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia. (PMID:34458856)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rbmxl1	ENSMUSG00000037070
mus_musculus	Gm7324	ENSMUSG00000049235
rattus_norvegicus	Rbmxl1	ENSRNOG00000062375

Paralogs (36): DAZAP1 (ENSG00000071626), CIRBP (ENSG00000099622), RBM23 (ENSG00000100461), RBM3 (ENSG00000102317), NCL (ENSG00000115053), TIA1 (ENSG00000116001), HNRNPA2B1 (ENSG00000122566), RBM19 (ENSG00000122965), RBM39 (ENSG00000131051), MSI1 (ENSG00000135097), HNRNPA1 (ENSG00000135486), HNRNPD (ENSG00000138668), HNRNPA1L2 (ENSG00000139675), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBM47 (ENSG00000163694), RBMY1F (ENSG00000169800), HNRNPA3 (ENSG00000170144), RBMXL2 (ENSG00000170748), RBM4B (ENSG00000173914), RBM4 (ENSG00000173933), RBMXL3 (ENSG00000175718), HNRNPA0 (ENSG00000177733), TRNAU1AP (ENSG00000180098), HNRNPAB (ENSG00000197451), HNRNPA1L3 (ENSG00000224578), RBMY1J (ENSG00000226941), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1B (ENSG00000242875), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

RNA binding motif protein, X-linked-like-1 — Q96E39 (reviewed: Q96E39)

Alternative names: Heterogeneous nuclear ribonucleoprotein G-like 1

All UniProt accessions (2): A0A1B0GUK8, Q96E39

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein which may be involved in pre-mRNA splicing.

Subcellular location. Nucleus.

Miscellaneous. According to some authors, RBMXL1 is a RBMX retrogene on chromosome X which is likely to be functional.

RefSeq proteins (2): NP_001156008, NP_062556 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR003954	RRM_euk-type	Domain
IPR012604	RBM1CTR	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR050441	RBM	Family

Pfam: PF00076, PF08081

UniProt features (14 total): compositionally biased region 8, modified residue 2, chain 1, domain 1, cross-link 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96E39-F1	54.25	0.06

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 (3): 88, 161, 80

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 122 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, AAGCAAT_MIR137, MORF_BRCA1, MORF_RAD51L3, MORF_PRKCA, GOBP_RNA_SPLICING, BASAKI_YBX1_TARGETS_DN, MORF_ATF2, chr1p22, MORF_PTEN, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOMF_MRNA_BINDING, MORF_IL16, MORF_DMPK

GO Biological Process (3): mRNA processing (GO:0006397), RNA splicing (GO:0008380), positive regulation of mRNA splicing, via spliceosome (GO:0048026)

GO Molecular Function (2): RNA binding (GO:0003723), nucleic acid binding (GO:0003676)

GO Cellular Component (4): spliceosomal complex (GO:0005681), nucleus (GO:0005634), organelle (GO:0043226), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
mRNA metabolic process	1
mRNA splicing, via spliceosome	1
positive regulation of RNA splicing	1
regulation of mRNA splicing, via spliceosome	1
positive regulation of mRNA processing	1
nucleic acid binding	1
binding	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
protein-containing complex	1

Protein interactions and networks

STRING

2174 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBMXL1	FRG1	Q14331	553
RBMXL1	LYRM2	Q9NU23	447
RBMXL1	GMCL2	Q8NEA9	436
RBMXL1	KYAT3	Q6YP21	432
RBMXL1	KHDRBS1	Q07666	405
RBMXL1	HNRNPC	P07910	394
RBMXL1	WBP11	Q9Y2W2	393
RBMXL1	PHOSPHO2	Q8TCD6	358
RBMXL1	ZNF66	Q6ZN08	350
RBMXL1	U2SURP	O15042	348
RBMXL1	MDN1	Q9NU22	322
RBMXL1	YTHDC2	Q9H6S0	320
RBMXL1	ZNF738	Q8NE65	307
RBMXL1	UTP14C	Q5TAP6	307
RBMXL1	YTHDC1	Q96MU7	307

IntAct

157 interactions, top by confidence:

A	B	Type	Score
N	HNRNPR	psi-mi:“MI:0914”(association)	0.730
DIDO1	OGT	psi-mi:“MI:0914”(association)	0.670
SUMO1	CBX4	psi-mi:“MI:0914”(association)	0.600
USP54	DYRK1A	psi-mi:“MI:0914”(association)	0.550
ILF2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
ZC3H18	AQR	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
SYNGAP1	SEC16A	psi-mi:“MI:0914”(association)	0.530
KIF2C	KIF2A	psi-mi:“MI:0914”(association)	0.530
SNRNP70	GTPBP1	psi-mi:“MI:0914”(association)	0.530
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
PAIP2B	CASC3	psi-mi:“MI:0914”(association)	0.530
ILF2	RRP8	psi-mi:“MI:0914”(association)	0.530
FBXW11	AHCYL1	psi-mi:“MI:0914”(association)	0.530
APOOL	MTX2	psi-mi:“MI:0914”(association)	0.530
SNRPC	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
EZH1	EPOP	psi-mi:“MI:0914”(association)	0.530
NEDD1	CEP290	psi-mi:“MI:0914”(association)	0.480
PPP2R2B	DDX3X	psi-mi:“MI:0914”(association)	0.460
Taf15	BTBD10	psi-mi:“MI:0914”(association)	0.350
AKAP5	MRPL43	psi-mi:“MI:0914”(association)	0.350
MATR3	BCLAF3	psi-mi:“MI:0914”(association)	0.350
BCLAF1	PABPN1	psi-mi:“MI:0914”(association)	0.350
Fus	DDX3X	psi-mi:“MI:0914”(association)	0.350
PPP1CC	CLIC1	psi-mi:“MI:0914”(association)	0.350
PPP1CB	PLEKHG3	psi-mi:“MI:0914”(association)	0.350

BioGRID (188): RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS), RBMXL1 (Affinity Capture-MS)

ESM2 similar proteins: A5A6M3, D4AE41, O22703, O75526, P30352, P35637, P38159, P56959, P60824, P60825, P60826, P62995, P62996, P62997, P78814, P84586, P92965, P92966, Q01560, Q01844, Q14011, Q24491, Q27294, Q28009, Q29RT0, Q3ZBT6, Q4P2Q5, Q4R7F0, Q4R813, Q4V898, Q54Y98, Q55FQ0, Q5RF83, Q61545, Q6IRQ4, Q7ZWA3, Q8L3X8, Q8RWN5, Q8VYA5, Q91VM5

Diamond homologs: A0A0A0LLY1, A0A0D1C8Z4, A5A6M3, C0HFE5, D3Z4I3, D4AE41, M0R7T6, O22703, O35698, O75526, O89086, O93235, P04147, P0C8Z4, P10979, P19682, P19683, P19684, P28644, P38159, P39697, P48809, P49310, P49311, P49313, P49314, P60824, P60825, P60826, P84586, P98179, Q03250, Q03251, Q03878, Q04836, Q05966, Q08473, Q08935, Q08937, Q14011

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 220 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
Transport of Mature Transcript to Cytoplasm	8	25.4×	6e-08
RNA Polymerase II Transcription Termination	9	16.5×	3e-07
mRNA 3’-end processing	10	16.4×	5e-08
mRNA Splicing	13	11.9×	9e-09
mRNA Polyadenylation	16	11.7×	3e-10
Transport of Mature mRNA derived from an Intron-Containing Transcript	9	11.4×	6e-06
Processing of Capped Intron-Containing Pre-mRNA	16	10.9×	4e-10
mRNA Splicing - Major Pathway	18	8.2×	1e-09

GO biological processes:

GO term	Partners	Fold	FDR
regulation of alternative mRNA splicing, via spliceosome	8	10.6×	3e-04
RNA splicing	13	6.2×	2e-04
mRNA splicing, via spliceosome	12	6.0×	3e-04
mRNA processing	12	5.1×	9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

1 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

532 predictions. Top by Δscore:

Variant	Effect	Δscore
1:88988250:A:AC	donor_gain	1.0000
1:88988251:C:CC	donor_gain	1.0000
1:88988889:T:TA	donor_gain	1.0000
1:88992582:CAC:C	donor_loss	1.0000
1:88988251:CAG:C	donor_gain	0.9900
1:88988348:CATG:C	acceptor_gain	0.9900
1:88988870:A:AC	donor_gain	0.9900
1:88988871:G:C	donor_gain	0.9900
1:88992583:A:AC	donor_gain	0.9900
1:88992584:C:CC	donor_gain	0.9900
1:88992584:CCTAT:C	donor_gain	0.9900
1:88992584:CCT:C	donor_gain	0.9800
1:88988352:C:CC	acceptor_gain	0.9700
1:88992885:A:AC	donor_gain	0.9700
1:88992886:C:CC	donor_gain	0.9700
1:88988350:TG:T	acceptor_gain	0.9600
1:88992583:AC:A	donor_gain	0.9600
1:88992584:CC:C	donor_gain	0.9600
1:88992609:C:A	donor_gain	0.9600
1:88992886:CGGCG:C	donor_gain	0.9600
1:88992584:CCTA:C	donor_gain	0.9500
1:88992588:T:C	donor_gain	0.9500
1:88992886:CGG:C	donor_gain	0.9500
1:88982558:T:A	donor_gain	0.9400
1:88992587:AT:A	donor_gain	0.9400
1:88988350:TGCT:T	acceptor_loss	0.9300
1:88988351:GCTA:G	acceptor_loss	0.9300
1:88988352:C:CG	acceptor_loss	0.9300
1:88991604:T:C	acceptor_gain	0.9300
1:88988251:CA:C	donor_gain	0.9200

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000650906 (1:88987312 G>A), RS1001014774 (1:88987409 C>A,T), RS1001310606 (1:88980856 A>G), RS1002214567 (1:88979141 T>A,C,G), RS1002306586 (1:88980171 A>G), RS1002438298 (1:88989009 G>T), RS1002464815 (1:88986792 G>C), RS1002576277 (1:88985564 C>A,G), RS1002595891 (1:88991673 T>C), RS1002680186 (1:88979666 A>G), RS1002691543 (1:88991797 G>A), RS1002783867 (1:88992490 G>A,C), RS1002880661 (1:88985915 T>A,G), RS1003714114 (1:88990452 A>G), RS1003774445 (1:88984135 G>A,C,T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	affects methylation	1
Calcitriol	decreases expression, affects cotreatment	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ivermectin	decreases expression	1
Ribonucleotides	affects binding	1
Testosterone	decreases expression, affects cotreatment	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	affects expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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