RBM27

Summary

RBM27 (RNA binding motif protein 27, HGNC:29243) is a protein-coding gene on chromosome 5q32, encoding RNA-binding protein 27 (Q9P2N5). May be involved in the turnover of nuclear polyadenylated (pA+) RNA.

Enables RNA binding activity. Predicted to be located in cytoplasm and nuclear speck. Predicted to be active in nucleus.

Source: NCBI Gene 54439 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 126 total
• MANE Select transcript: NM_018989

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29243
Approved symbol	RBM27
Name	RNA binding motif protein 27
Location	5q32
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1311, ARRS1, Psc1, ZC3H20
Ensembl gene	ENSG00000091009
Ensembl biotype	protein_coding
OMIM	620082
Entrez	54439

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 retained_intron

ENST00000265271, ENST00000508019, ENST00000861564, ENST00000861565, ENST00000939623, ENST00000939624, ENST00000939625, ENST00000939626, ENST00000941083, ENST00000941084

RefSeq mRNA: 1 — MANE Select: NM_018989 NM_018989

CCDS: CCDS43378

Canonical transcript exons

ENST00000265271 — 21 exons

Exon	Start	End
ENSE00000766797	146284622	146284732
ENSE00000972717	146251711	146251875
ENSE00001417784	146203605	146203824
ENSE00001553467	146285947	146289223
ENSE00003713221	146269207	146269281
ENSE00003715322	146260745	146260898
ENSE00003721403	146218985	146219103
ENSE00003725754	146267649	146267768
ENSE00003729285	146258449	146258593
ENSE00003731012	146263491	146263631
ENSE00003732963	146230657	146230917
ENSE00003733423	146261510	146261806
ENSE00003736356	146228946	146229037
ENSE00003737035	146254943	146255092
ENSE00003738400	146271483	146271674
ENSE00003738569	146229717	146229910
ENSE00003739985	146223403	146223527
ENSE00003742838	146269420	146269584
ENSE00003744972	146233450	146233743
ENSE00003748316	146237298	146237432
ENSE00003750649	146270954	146271058

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 94.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.9433 / max 293.8358, expressed in 1811 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
59211	15.0643	1798
59210	6.0034	1675
59212	1.8756	958

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
caput epididymis	UBERON:0004358	94.71	gold quality
cauda epididymis	UBERON:0004360	94.10	gold quality
secondary oocyte	CL:0000655	93.79	gold quality
corpus epididymis	UBERON:0004359	93.00	gold quality
cardiac muscle of right atrium	UBERON:0003379	92.93	gold quality
calcaneal tendon	UBERON:0003701	92.80	gold quality
tibialis anterior	UBERON:0001385	92.51	gold quality
left ventricle myocardium	UBERON:0006566	92.20	gold quality
superficial temporal artery	UBERON:0001614	91.98	gold quality
upper arm skin	UBERON:0004263	91.76	gold quality
mucosa of paranasal sinus	UBERON:0005030	91.74	gold quality
ileal mucosa	UBERON:0000331	91.51	gold quality
bronchial epithelial cell	CL:0002328	91.50	gold quality
bronchus	UBERON:0002185	91.02	gold quality
deltoid	UBERON:0001476	90.54	gold quality
lower lobe of lung	UBERON:0008949	90.48	gold quality
pigmented layer of retina	UBERON:0001782	90.08	gold quality
retina	UBERON:0000966	90.06	gold quality
mucosa of sigmoid colon	UBERON:0004993	90.01	gold quality
seminal vesicle	UBERON:0000998	89.61	gold quality
layer of synovial tissue	UBERON:0007616	89.48	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	89.25	gold quality
biceps brachii	UBERON:0001507	89.18	gold quality
colonic mucosa	UBERON:0000317	89.09	gold quality
visceral pleura	UBERON:0002401	89.06	gold quality
skin of hip	UBERON:0001554	88.94	gold quality
upper leg skin	UBERON:0004262	88.93	gold quality
trabecular bone tissue	UBERON:0002483	88.83	gold quality
corpus callosum	UBERON:0002336	88.75	gold quality
parietal pleura	UBERON:0002400	88.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

282 targeting RBM27, 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-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4789-3P	99.99	70.75	2484

Literature-anchored findings (GeneRIF, showing 2)

• three additional proteins required for Poly(A) Tail eXosome Targeting (PAXT) function: ZC3H3, RBM26 and RBM27 along with the known PAXT-associated protein, PABPN1, were identified. (PMID:31950173)
• PAPgamma associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs. (PMID:37875486)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbm27	ENSDARG00000060521
mus_musculus	Rbm27	ENSMUSG00000024491
rattus_norvegicus	Rbm27	ENSRNOG00000027250
drosophila_melanogaster	swm	FBGN0002044
caenorhabditis_elegans		WBGENE00015143

Paralogs (1): RBM26 (ENSG00000139746)

Protein

Protein identifiers

RNA-binding protein 27 — Q9P2N5 (reviewed: Q9P2N5)

Alternative names: RNA-binding motif protein 27

All UniProt accessions (1): Q9P2N5

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the turnover of nuclear polyadenylated (pA+) RNA.

Subcellular location. Cytoplasm. Nucleus speckle.

Domain organisation. The RRM domain mediates integration into cytospeckles.

RefSeq proteins (1): NP_061862* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR000571	Znf_CCCH	Domain
IPR002483	PWI_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034451	RBM27_RRM	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR045137	RBM26/27	Family

Pfam: PF00076, PF00642, PF01480

UniProt features (25 total): compositionally biased region 10, region of interest 6, modified residue 5, chain 1, domain 1, zinc finger region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2N5-F1	55.54	0.10

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 (5): 447, 455, 927, 1012, 1020

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9930044	Nuclear RNA decay

MSigDB gene sets: 169 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GSE45365_NK_CELL_VS_CD8_TCELL_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, chr5q32, REACTOME_METABOLISM_OF_RNA, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, GOCC_RIBONUCLEOPROTEIN_GRANULE, HAMAI_APOPTOSIS_VIA_TRAIL_UP, GOCC_SUPRAMOLECULAR_COMPLEX, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, ASH1L_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (4): RNA binding (GO:0003723), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear speck (GO:0016607)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
nuclear ribonucleoprotein granule	1

Protein interactions and networks

STRING

1686 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM27	ZFC3H1	O60293	622
RBM27	NCBP2	P52298	552
RBM27	SRRT	Q9BXP5	530
RBM27	POLR2L	P52436	472
RBM27	ZC3H3	Q8IXZ2	469
RBM27	RBM7	Q9Y580	464
RBM27	MTREX	P42285	459
RBM27	ZCCHC8	Q6NZY4	451
RBM27	PSMA2	P25787	447
RBM27	TCERG1	O14776	446
RBM27	PABPN1	Q86U42	438
RBM27	DELE1	Q14154	436
RBM27	SH3RF2	Q8TEC5	414
RBM27	ZFP2	Q6ZN57	380
RBM27	ZFP3	Q96NJ6	380

IntAct

145 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:0914”(association)	0.900
CHCHD10	CLPX	psi-mi:“MI:0914”(association)	0.640
ZNF414	AHCYL1	psi-mi:“MI:0914”(association)	0.640
SUMO1	CBX4	psi-mi:“MI:0914”(association)	0.600
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
NCBP3	SAP18	psi-mi:“MI:0914”(association)	0.530
FHL2	CNOT1	psi-mi:“MI:0914”(association)	0.530
TNFRSF13B	TNFRSF10B	psi-mi:“MI:0914”(association)	0.530
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
CLEC3A	ZZEF1	psi-mi:“MI:0914”(association)	0.530
SRPK2	RRP9	psi-mi:“MI:0914”(association)	0.530
SRPK1	DROSHA	psi-mi:“MI:0914”(association)	0.530
EZH1	EPOP	psi-mi:“MI:0914”(association)	0.530
RPL13	RRP8	psi-mi:“MI:0914”(association)	0.530
RPLP0	GTPBP10	psi-mi:“MI:0914”(association)	0.530
YWHAZ	WDR62	psi-mi:“MI:0914”(association)	0.350
THOC1	TARS3	psi-mi:“MI:0914”(association)	0.350
ZFC3H1	UNC119B	psi-mi:“MI:0914”(association)	0.350
THOC7	ALYREF	psi-mi:“MI:0914”(association)	0.350
Plk2	NES	psi-mi:“MI:0914”(association)	0.350
Srsf1	SRRM1	psi-mi:“MI:0914”(association)	0.350
ACTR2	PPP1R12A	psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
k8	RGL2	psi-mi:“MI:0914”(association)	0.350
PDHA1		psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (179): RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), NCBP1 (Co-fractionation), PCF11 (Co-fractionation), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS), RBM27 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WPF7, A0A0R4IBL7, O09000, O54972, O70305, O75081, O75376, P15806, P15881, P15884, P15923, P21677, P30985, P51514, P98180, Q05AQ8, Q14157, Q14687, Q1LY51, Q2VPM4, Q3U3C9, Q4KKX4, Q4VCS5, Q566L4, Q5F3B1, Q5SFM8, Q5T6F2, Q60722, Q60974, Q61286, Q62655, Q6DIH5, Q7ZWN6, Q7ZXS3, Q80X50, Q86YP4, Q8BZ47, Q8CHY6, Q8IXK0, Q8VHG2

Diamond homologs: Q0JDM0, Q5SFM8, Q9LVX1, Q9P2N5, Q2T9I5, Q5T8P6, Q6NZN0, Q9USP9, O13759, Q9VIV2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 194 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	7	19.2×	4e-06
mRNA 3’-end processing	12	17.0×	1e-09
RNA Polymerase II Transcription Termination	9	14.2×	1e-06
Transport of Mature mRNA derived from an Intron-Containing Transcript	10	10.9×	2e-06
SARS-CoV-1-host interactions	7	8.8×	4e-04
mRNA Splicing	11	8.7×	4e-06
Nonsense-Mediated Decay (NMD)	5	8.4×	6e-03
Processing of Capped Intron-Containing Pre-mRNA	14	8.3×	2e-07

GO biological processes:

GO term	Partners	Fold	FDR
regulation of mRNA splicing, via spliceosome	6	30.6×	7e-06
negative regulation of mRNA splicing, via spliceosome	6	26.4×	2e-05
RNA splicing	23	11.7×	3e-15
negative regulation of translation	9	10.1×	4e-05
ribosomal small subunit biogenesis	7	9.2×	1e-03
mRNA transport	6	9.1×	5e-03
mRNA processing	20	9.1×	4e-11
cytoplasmic translation	8	8.5×	7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	97
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2659 predictions. Top by Δscore:

Variant	Effect	Δscore
5:146203822:GAT:G	donor_gain	1.0000
5:146203823:AT:A	donor_gain	1.0000
5:146203824:TGTG:T	donor_loss	1.0000
5:146203825:G:GG	donor_gain	1.0000
5:146203825:GT:G	donor_loss	1.0000
5:146203825:GTGA:G	donor_gain	1.0000
5:146203829:G:GG	donor_gain	1.0000
5:146218974:T:TA	acceptor_gain	1.0000
5:146218979:A:AG	acceptor_gain	1.0000
5:146218980:A:G	acceptor_gain	1.0000
5:146218982:TAG:T	acceptor_loss	1.0000
5:146218982:TAGAT:T	acceptor_loss	1.0000
5:146218983:A:AC	acceptor_loss	1.0000
5:146218983:A:AG	acceptor_gain	1.0000
5:146218984:G:GC	acceptor_gain	1.0000
5:146218984:G:GT	acceptor_gain	1.0000
5:146218984:GA:G	acceptor_gain	1.0000
5:146218984:GAT:G	acceptor_gain	1.0000
5:146218984:GATGT:G	acceptor_gain	1.0000
5:146219100:AAAGG:A	donor_loss	1.0000
5:146219101:AAGG:A	donor_loss	1.0000
5:146219102:AGG:A	donor_loss	1.0000
5:146219102:AGGTA:A	donor_loss	1.0000
5:146219103:GGTAA:G	donor_loss	1.0000
5:146219104:G:GA	donor_loss	1.0000
5:146219105:T:G	donor_loss	1.0000
5:146223401:A:AG	acceptor_gain	1.0000
5:146223402:G:GA	acceptor_gain	1.0000
5:146223402:GA:G	acceptor_gain	1.0000
5:146223402:GAA:G	acceptor_gain	1.0000

AlphaMissense

6895 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:146203791:T:C	L9P	1.000
5:146203803:T:C	L13P	1.000
5:146203815:T:C	L17P	1.000
5:146219008:T:C	L28S	1.000
5:146219011:C:A	A29D	1.000
5:146219020:T:A	V32D	1.000
5:146219029:T:C	L35P	1.000
5:146219032:T:A	V36D	1.000
5:146219070:T:C	C49R	1.000
5:146219072:T:G	C49W	1.000
5:146219083:T:A	L53H	1.000
5:146219083:T:C	L53P	1.000
5:146219091:T:C	F56L	1.000
5:146219092:T:C	F56S	1.000
5:146219092:T:G	F56C	1.000
5:146219093:T:A	F56L	1.000
5:146219093:T:G	F56L	1.000
5:146223415:T:C	F64S	1.000
5:146223427:T:C	L68P	1.000
5:146230902:T:A	C279S	1.000
5:146230902:T:C	C279R	1.000
5:146230903:G:C	C279S	1.000
5:146230904:C:G	C279W	1.000
5:146233461:T:A	C288S	1.000
5:146233461:T:C	C288R	1.000
5:146233462:G:A	C288Y	1.000
5:146233462:G:C	C288S	1.000
5:146233463:T:G	C288W	1.000
5:146233479:T:A	C294S	1.000
5:146233479:T:C	C294R	1.000

dbSNP variants (sampled 300 via entrez): RS1000025599 (5:146233100 T>A), RS1000031560 (5:146270844 C>T), RS1000045220 (5:146236301 A>G), RS1000200744 (5:146230007 G>A,C,T), RS1000229725 (5:146274804 A>G), RS1000290645 (5:146250667 A>G), RS1000304473 (5:146208760 A>C), RS1000329288 (5:146256647 C>A,T), RS1000346588 (5:146263937 T>G), RS1000372463 (5:146264123 A>G), RS1000455870 (5:146268040 C>T), RS1000497464 (5:146226665 G>A), RS1000507233 (5:146280950 CG>C), RS1000514319 (5:146261049 T>C), RS1000515460 (5:146251673 T>A)

Disease associations

OMIM: gene MIM:620082 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST008359_7	Response to cognitive-behavioural therapy in anxiety disorder	4.000000e-06
GCST90002404_216	Red cell distribution width	7.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007820	cognitive behavioural therapy
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
methylmercuric chloride	decreases expression	1
arsenite	affects binding, decreases reaction	1
di-n-butylphosphoric acid	affects expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
jinfukang	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Methotrexate	increases expression	1
Ribonucleotides	affects binding	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	affects expression	1
Aflatoxin M1	decreases expression	1
Asbestos, Serpentine	decreases methylation	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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