RTL9

Summary

RTL9 (retrotransposon Gag like 9, HGNC:29245) is a protein-coding gene on chromosome Xq23, encoding Retrotransposon Gag-like protein 9 (Q8NET4).

At a glance

• Clinical variants (ClinVar): 221 total
• MANE Select transcript: NM_001385449

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29245
Approved symbol	RTL9
Name	retrotransposon Gag like 9
Location	Xq23
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1318, Mart9, Mar9, SIRH10
Ensembl gene	ENSG00000243978
Ensembl biotype	protein_coding
OMIM	300965
Entrez	57529

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000465301, ENST00000520821, ENST00000540313

RefSeq mRNA: 2 — MANE Select: NM_001385449 NM_001385449, NM_020769

CCDS: CCDS14552

Canonical transcript exons

ENST00000520821 — 4 exons

Exon	Start	End
ENSE00002110296	110450567	110454664
ENSE00002123383	110445153	110445268
ENSE00003967359	110455202	110456334
ENSE00003967360	110358848	110358916

Expression profiles

Bgee: expression breadth broad, 83 present calls, max score 77.55.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0735 / max 52.7769, expressed in 14 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197266	0.0466	9
197265	0.0205	4
197264	0.0064	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibialis anterior	UBERON:0001385	77.55	silver quality
right testis	UBERON:0004534	74.82	gold quality
left testis	UBERON:0004533	72.19	gold quality
testis	UBERON:0000473	72.10	gold quality
pancreatic ductal cell	CL:0002079	69.01	silver quality
ventricular zone	UBERON:0003053	66.84	gold quality
ileal mucosa	UBERON:0000331	64.56	silver quality
cortical plate	UBERON:0005343	63.02	gold quality
deltoid	UBERON:0001476	62.59	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	60.77	gold quality
lower lobe of lung	UBERON:0008949	57.87	silver quality
ganglionic eminence	UBERON:0004023	57.08	gold quality
adrenal tissue	UBERON:0018303	57.07	gold quality
hypothalamus	UBERON:0001898	57.00	gold quality
adult organism	UBERON:0007023	57.00	silver quality
epithelial cell of pancreas	CL:0000083	55.74	gold quality
cardiac muscle of right atrium	UBERON:0003379	55.53	gold quality
nucleus accumbens	UBERON:0001882	55.31	gold quality
heart left ventricle	UBERON:0002084	54.61	gold quality
right ovary	UBERON:0002118	54.44	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
cardiac ventricle	UBERON:0002082	54.12	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
left ovary	UBERON:0002119	53.89	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
oocyte	CL:0000023	53.42	gold quality
ovary	UBERON:0000992	52.84	gold quality
prefrontal cortex	UBERON:0000451	52.71	gold quality
substantia nigra	UBERON:0002038	51.21	gold quality
heart	UBERON:0000948	50.92	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

92 targeting RTL9, 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-6748-5P	100.00	65.81	1057
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-6759-5P	99.99	66.54	785
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-219A-5P	99.91	73.36	735

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	vap	ENSDARG00000088975
mus_musculus	Rtl9	ENSMUSG00000085584
rattus_norvegicus	Rtl9	ENSRNOG00000049853
drosophila_melanogaster	mesh	FBGN0051004
caenorhabditis_elegans		WBGENE00010047
caenorhabditis_elegans		WBGENE00010540
caenorhabditis_elegans		WBGENE00011175

Paralogs (2): SUSD2 (ENSG00000099994), MUC4 (ENSG00000145113)

Protein

Protein identifiers

Retrotransposon Gag-like protein 9 — Q8NET4 (reviewed: Q8NET4)

Alternative names: Retrotransposon gag domain-containing protein 1, Tumor antigen BJ-HCC-23

All UniProt accessions (2): E5RKA1, Q8NET4

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. RTL9 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_001372378, NP_065820 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR042919	RTL9	Family

UniProt features (9 total): region of interest 5, compositionally biased region 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NET4-F1	39.37	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 103 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, RNGTGGGC_UNKNOWN, MYAATNNNNNNNGGC_UNKNOWN, AP1_01, FREAC2_01, HNF3ALPHA_Q6, GGGNRMNNYCAT_UNKNOWN, RORA1_01, FOXO4_01, FOXO1_01, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, CAGCTG_AP4_Q5, FOXD3_01, AP1_Q4_01, HEN1_01

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

718 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RTL9	RTL6	Q6ICC9	810
RTL9	RTL4	Q6ZR62	716
RTL9	NUTM2G	Q5VZR2	664
RTL9	RTL8C	A6ZKI3	606
RTL9	AMMECR1	Q9Y4X0	600
RTL9	LDOC1	O95751	599
RTL9	TMEM164	Q5U3C3	578
RTL9	NUGGC	Q68CJ6	541
RTL9	MAP7D2	Q96T17	505
RTL9	RALGPS1	Q5JS13	486
RTL9	APOLD1	Q96LR9	424
RTL9	RTL5	Q5HYW3	416
RTL9	ZCCHC3	Q9NUD5	402
RTL9	ZC3H7B	Q9UGR2	400
RTL9	RTL1	A6NKG5	398

IntAct

12 interactions, top by confidence:

A	B	Type	Score
HSF1	KPNA3	psi-mi:“MI:0914”(association)	0.640
CBX6	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
PRDX2	PRDX3	psi-mi:“MI:0914”(association)	0.510
ANKRA2	RTL9	psi-mi:“MI:0407”(direct interaction)	0.440
CIMIP4	ATE1	psi-mi:“MI:0914”(association)	0.350
UGT1A7	FGFR1	psi-mi:“MI:0914”(association)	0.350
UGT1A7	ADAM10	psi-mi:“MI:0914”(association)	0.350
CD247	DDX1	psi-mi:“MI:0914”(association)	0.350
CEP152	CNOT1	psi-mi:“MI:2364”(proximity)	0.270
RTL9	HSF1	psi-mi:“MI:0915”(physical association)	0.000
PRDX2	RTL9	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): RGAG1 (Proximity Label-MS), RGAG1 (Proximity Label-MS), RGAG1 (Affinity Capture-MS), RGAG1 (Affinity Capture-MS), HSF1 (Affinity Capture-MS), RGAG1 (Affinity Capture-MS), RGAG1 (Affinity Capture-MS), RGAG1 (Affinity Capture-MS), RGAG1 (Affinity Capture-MS), NASP (Cross-Linking-MS (XL-MS)), RGAG1 (Affinity Capture-MS), RGAG1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQI7, A0A494C071, A6QL64, A6ZXT5, A7XUY5, E2RYF6, E2RYF7, O60732, O88799, P06916, P12021, P18583, P41809, P43537, P47179, P53353, Q00130, Q02496, Q02505, Q04893, Q05049, Q12459, Q14242, Q32KG4, Q4ZJY7, Q4ZJZ0, Q54QZ8, Q5H9R4, Q5H9T9, Q5JPF3, Q5SSG8, Q5XHX6, Q60528, Q63661, Q685J3, Q6P902, Q86VQ3, Q8JZM8, Q8N307, Q8NET4

Diamond homologs: Q32KG4, Q8NET4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	168
Likely benign	14
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

716 predictions. Top by Δscore:

Variant	Effect	Δscore
X:110419132:GTGG:G	donor_gain	1.0000
X:110419133:TGGG:T	donor_loss	1.0000
X:110419134:GG:G	donor_gain	1.0000
X:110419135:GG:G	donor_gain	1.0000
X:110419136:G:GA	donor_loss	1.0000
X:110445110:T:TA	acceptor_gain	1.0000
X:110419133:TGG:T	donor_gain	0.9900
X:110419134:GGG:G	donor_gain	0.9900
X:110419136:G:GG	donor_gain	0.9900
X:110454599:GCCT:G	donor_gain	0.9900
X:110455194:A:AG	acceptor_gain	0.9900
X:110455197:CCCA:C	acceptor_loss	0.9900
X:110455198:CCA:C	acceptor_loss	0.9900
X:110455200:A:AG	acceptor_gain	0.9900
X:110455200:A:AT	acceptor_loss	0.9900
X:110455201:G:A	acceptor_loss	0.9900
X:110455201:G:GA	acceptor_gain	0.9900
X:110455201:GC:G	acceptor_gain	0.9900
X:110455201:GCACC:G	acceptor_gain	0.9900
X:110445111:G:A	acceptor_gain	0.9800
X:110454662:G:GT	donor_gain	0.9800
X:110455195:C:G	acceptor_gain	0.9800
X:110419131:TGTGG:T	donor_gain	0.9700
X:110419132:GTGGG:G	donor_gain	0.9700
X:110419133:TGGGT:T	donor_gain	0.9700
X:110445147:T:G	acceptor_gain	0.9700
X:110454620:G:GT	donor_gain	0.9700
X:110455201:GCA:G	acceptor_gain	0.9700
X:110455201:GCAC:G	acceptor_gain	0.9700
X:110444492:T:TA	donor_gain	0.9600

AlphaMissense

558 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:110450645:T:C	F10L	0.758
X:110450647:C:A	F10L	0.758
X:110450647:C:G	F10L	0.758
X:110450828:T:C	F71L	0.717
X:110450830:T:A	F71L	0.717
X:110450830:T:G	F71L	0.717
X:110450699:T:C	F28L	0.662
X:110450701:C:A	F28L	0.662
X:110450701:C:G	F28L	0.662

dbSNP variants (sampled 300 via entrez): RS1000053110 (X:110362214 C>G,T), RS1000103740 (X:110361767 A>T), RS1000103882 (X:110423688 T>G), RS1000164254 (X:110445362 A>G), RS1000169722 (X:110421267 G>A), RS1000279452 (X:110371401 A>G), RS1000421008 (X:110360224 C>G), RS1000476139 (X:110424177 A>G), RS1000489570 (X:110445776 G>A), RS1000501363 (X:110448302 C>T), RS1000542869 (X:110395351 C>T), RS1000595426 (X:110372130 G>A,T), RS1000599925 (X:110386136 G>T), RS1000679670 (X:110363173 T>C), RS1000682331 (X:110436682 C>T)

Disease associations

OMIM: gene MIM:300965 | 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

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

Chemical	Actions (top 5)	PubMed papers
2,4,6-tribromophenol	decreases expression	1
methyleugenol	decreases expression	1
sodium arsenite	increases expression	1
tetrabromobisphenol A	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Caffeine	increases phosphorylation	1
Cisplatin	increases expression	1
Estradiol	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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