RTL5

Summary

RTL5 (retrotransposon Gag like 5, HGNC:29430) is a protein-coding gene on chromosome Xq13.1, encoding Retrotransposon Gag-like protein 5 (Q5HYW3).

At a glance

• MANE Select transcript: NM_001405151

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29430
Approved symbol	RTL5
Name	retrotransposon Gag like 5
Location	Xq13.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA2001, Mar5, Mart5, SIRH8
Ensembl gene	ENSG00000242732
Ensembl biotype	protein_coding
OMIM	301135
Entrez	340526

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 nonsense_mediated_decay, 1 protein_coding

ENST00000479991, ENST00000609883

RefSeq mRNA: 2 — MANE Select: NM_001405151 NM_001024455, NM_001405151

CCDS: CCDS55446

Canonical transcript exons

ENST00000609883 — 1 exons

Exon	Start	End
ENSE00003706956	72127110	72131915

Expression profiles

Bgee: expression breadth ubiquitous, 216 present calls, max score 91.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.8434 / max 143.5361, expressed in 1246 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199574	4.8434	1246

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	91.13	gold quality
cerebellar hemisphere	UBERON:0002245	91.08	gold quality
cerebellar cortex	UBERON:0002129	91.06	gold quality
cerebellum	UBERON:0002037	90.83	gold quality
ganglionic eminence	UBERON:0004023	90.35	gold quality
pituitary gland	UBERON:0000007	89.62	gold quality
adenohypophysis	UBERON:0002196	89.06	gold quality
cerebellar vermis	UBERON:0004720	87.02	silver quality
islet of Langerhans	UBERON:0000006	86.81	gold quality
ventricular zone	UBERON:0003053	85.89	gold quality
lateral nuclear group of thalamus	UBERON:0002736	85.36	gold quality
right frontal lobe	UBERON:0002810	84.79	gold quality
caudate nucleus	UBERON:0001873	84.58	gold quality
sural nerve	UBERON:0015488	84.49	gold quality
putamen	UBERON:0001874	84.37	gold quality
nucleus accumbens	UBERON:0001882	84.04	gold quality
brain	UBERON:0000955	83.93	gold quality
frontal cortex	UBERON:0001870	83.69	gold quality
superior frontal gyrus	UBERON:0002661	83.59	gold quality
prefrontal cortex	UBERON:0000451	83.36	gold quality
forebrain	UBERON:0001890	83.30	gold quality
neocortex	UBERON:0001950	83.20	gold quality
endothelial cell	CL:0000115	83.07	silver quality
postcentral gyrus	UBERON:0002581	82.94	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	82.90	gold quality
entorhinal cortex	UBERON:0002728	82.75	gold quality
cerebral cortex	UBERON:0000956	82.73	gold quality
hypothalamus	UBERON:0001898	82.63	gold quality
middle temporal gyrus	UBERON:0002771	82.61	gold quality
parietal lobe	UBERON:0001872	82.55	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

123 targeting RTL5, 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-4455	100.00	65.48	1587
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-1299	99.77	71.24	2389

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rtl5	ENSMUSG00000049191
rattus_norvegicus	Rtl5	ENSRNOG00000045779

Paralogs (10): RTL8C (ENSG00000134590), RTL3 (ENSG00000179300), LDOC1 (ENSG00000182195), RTL4 (ENSG00000187823), RTL6 (ENSG00000188636), RTL8A (ENSG00000203950), RTL8B (ENSG00000212747), RTL10 (ENSG00000215012), PEG10 (ENSG00000242265), RTL1 (ENSG00000254656)

Protein

Protein identifiers

Retrotransposon Gag-like protein 5 — Q5HYW3 (reviewed: Q5HYW3)

Alternative names: Retrotransposon gag domain-containing protein 4

All UniProt accessions (1): Q5HYW3

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. RTL5 is one of at least 11 genes called Mar or Mart related to long terminal repeat retrotransposons. They do not correspond to functional retrotransposons, but rather to neofunctionalized retrotransposons genes.

RefSeq proteins (2): NP_001019626, NP_001392080* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032549	RTL1/1-8/LDOC_capsid-like	Domain
IPR032567	RTL1-rel	Family

Pfam: PF16297

UniProt features (12 total): compositionally biased region 8, region of interest 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5HYW3-F1	64.32	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 84 (showing top): BENPORATH_ES_WITH_H3K27ME3, GGTGTGT_MIR329, ACTGCAG_MIR173P, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, ZHAN_MULTIPLE_MYELOMA_CD1_UP, KOYAMA_SEMA3B_TARGETS_UP, ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP, DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN, chrXq13, GSE13522_WT_VS_IFNAR_KO_SKIN_DN, MIR3529_3P, MIR545_3P, MIR3941, MIR1299, MIR6739_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

538 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RTL5	RTL8C	A6ZKI3	672
RTL5	RTL8A	Q9BWD3	528
RTL5	RTL4	Q6ZR62	518
RTL5	RTL9	Q8NET4	416
RTL5	PNMA5	Q96PV4	409
RTL5	EOLA1	Q8TE69	398
RTL5	ST8SIA6	P61647	386
RTL5	PNMA8A	Q86V59	369
RTL5	ZCCHC3	Q9NUD5	364
RTL5	TBXT	O15178	358
RTL5	RTL6	Q6ICC9	356
RTL5	RNASE8	Q8TDE3	350
RTL5	SLC10A3	P09131	347
RTL5	ENAH	Q8N8S7	347
RTL5	RTL3	Q8N8U3	343

IntAct

0 interactions, top by confidence:

BioGRID (6): RGAG4 (Negative Genetic), RGAG4 (Positive Genetic), RGAG4 (Proximity Label-MS), RGAG4 (Proximity Label-MS), RGAG4 (Proximity Label-MS), RGAG4 (Proximity Label-MS)

ESM2 similar proteins: A4FUB7, A6NKG5, O60290, O89290, O91080, P03975, P04023, P04584, P05896, P05897, P0C691, P0CG32, P11365, P12451, P12502, P15833, P17192, P17757, P18096, P19505, P20876, P24107, P24740, P30028, P35125, Q09PK2, Q1A267, Q4R6I1, Q52QI2, Q53RT3, Q5DTT4, Q5HYW3, Q5HZA3, Q66403, Q66H30, Q6PEW1, Q74120, Q76634, Q77373, Q7M732

Diamond homologs: A6NKG5, A6ZKI3, O95751, Q17QF6, Q17RB0, Q1JQ94, Q52QI2, Q5DTZ0, Q5HYW3, Q6SEH4, Q6SEH5, Q7M732, Q7TPY9, Q9BWD3, Q32KG4, Q505G4, Q5DTT4, Q6ICC9, Q86TG7, Q8N8U3, Q5R6M8, Q7L3V2, Q6P1Y1, Q7TN75

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

243 predictions. Top by Δscore:

Variant	Effect	Δscore
X:72131831:G:GA	donor_gain	0.8500
X:72131511:GCTGT:G	donor_gain	0.8400
X:72131830:T:TA	donor_gain	0.8300
X:72131814:G:GT	donor_gain	0.8100
X:72131043:G:GT	donor_gain	0.7900
X:72131787:C:T	donor_gain	0.7900
X:72131744:G:GT	donor_gain	0.7800
X:72131407:G:GT	donor_gain	0.7700
X:72130794:AC:A	donor_gain	0.7600
X:72131610:G:GT	donor_gain	0.7600
X:72131746:C:T	donor_gain	0.7600
X:72131439:G:GT	donor_gain	0.7400
X:72131888:G:GT	donor_gain	0.7300
X:72131638:G:T	donor_gain	0.7200
X:72131408:A:T	donor_gain	0.7100
X:72131646:G:GT	donor_gain	0.7100
X:72131798:G:GT	donor_gain	0.7000
X:72131638:G:GT	donor_gain	0.6900
X:72131663:C:T	donor_gain	0.6900
X:72130560:G:T	donor_gain	0.6800
X:72131352:G:GT	donor_gain	0.6800
X:72131694:C:T	donor_gain	0.6800
X:72130630:C:G	acceptor_gain	0.6500
X:72131515:T:G	donor_gain	0.6500
X:72131508:G:GT	donor_gain	0.6400
X:72131771:A:T	donor_gain	0.6400
X:72131832:GCG:G	donor_gain	0.6400
X:72131637:G:GT	donor_gain	0.6300
X:72131702:G:GT	donor_gain	0.6300
X:72131403:C:T	donor_gain	0.6200

AlphaMissense

3740 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:72130642:A:G	L300P	0.997
X:72130742:A:G	W267R	0.997
X:72130742:A:T	W267R	0.997
X:72130714:A:G	F276S	0.996
X:72131488:A:G	L18P	0.996
X:72130713:G:C	F276L	0.995
X:72130713:G:T	F276L	0.995
X:72130715:A:G	F276L	0.995
X:72130740:C:A	W267C	0.995
X:72130740:C:G	W267C	0.995
X:72131509:A:G	L11P	0.995
X:72131043:G:C	F166L	0.994
X:72131043:G:T	F166L	0.994
X:72131045:A:G	F166L	0.994
X:72131509:A:T	L11H	0.994
X:72130767:A:C	F258L	0.993
X:72130767:A:T	F258L	0.993
X:72130769:A:G	F258L	0.993
X:72130678:A:G	L288P	0.992
X:72131501:C:G	A14P	0.991
X:72130631:A:G	C304R	0.990
X:72131073:A:C	F156L	0.990
X:72131073:A:T	F156L	0.990
X:72131075:A:G	F156L	0.990
X:72131467:A:G	L25P	0.990
X:72131496:A:C	N15K	0.990
X:72131496:A:T	N15K	0.990
X:72130768:A:G	F258S	0.989
X:72131476:A:G	L22S	0.989
X:72130711:A:G	L277P	0.988

dbSNP variants (sampled 300 via entrez): RS1000974492 (X:72129395 T>C), RS1000991693 (X:72132425 T>C), RS1001868107 (X:72132458 T>C), RS1002432998 (X:72132993 G>C), RS1004099478 (X:72132930 C>T), RS1004846103 (X:72131464 C>A,T), RS1005183523 (X:72133522 T>C), RS1005235747 (X:72133119 A>G), RS1006467354 (X:72126671 T>C), RS1007203151 (X:72133701 G>T), RS1007234088 (X:72133203 C>G,T), RS1007510867 (X:72128088 G>A,C), RS1008284802 (X:72126939 C>T), RS1008568955 (X:72129655 G>A,T), RS1008575848 (X:72129332 G>A)

Disease associations

OMIM: gene MIM:301135 | 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

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	2
Benzo(a)pyrene	affects methylation, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
aristolochic acid I	increases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
2-methyl-4-isothiazolin-3-one	increases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	increases expression	1
Sunitinib	increases expression	1
Carbamazepine	affects expression	1
Cisplatin	affects cotreatment, increases expression	1
Doxorubicin	increases expression	1
Ethinyl Estradiol	decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	decreases expression	1
Urethane	increases expression	1
Valproic Acid	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1

Clinical trials (associated diseases)

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