TIGD3

Summary

TIGD3 (tigger transposable element derived 3, HGNC:18334) is a protein-coding gene on chromosome 11q13.1, encoding Tigger transposable element-derived protein 3 (Q6B0B8).

The protein encoded by this gene belongs to the tigger subfamily of the pogo superfamily of DNA-mediated transposons in humans. These proteins are related to DNA transposons found in fungi and nematodes, and more distantly to the Tc1 and mariner transposases. They are also very similar to the major mammalian centromere protein B. The exact function of this gene is not known.

Source: NCBI Gene 220359 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 70 total
• MANE Select transcript: NM_145719

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18334
Approved symbol	TIGD3
Name	tigger transposable element derived 3
Location	11q13.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000173825
Ensembl biotype	protein_coding
OMIM	619084
Entrez	220359

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000309880, ENST00000929631, ENST00000929632

RefSeq mRNA: 1 — MANE Select: NM_145719 NM_145719

CCDS: CCDS8101

Canonical transcript exons

ENST00000309880 — 2 exons

Exon	Start	End
ENSE00003988451	65354751	65354957
ENSE00003988457	65355793	65357613

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 79.70.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2481 / max 25.0367, expressed in 109 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
115070	0.2481	109

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.70	gold quality
blood	UBERON:0000178	73.23	gold quality
cortical plate	UBERON:0005343	70.57	gold quality
granulocyte	CL:0000094	70.52	gold quality
cerebellar hemisphere	UBERON:0002245	70.49	gold quality
cerebellar cortex	UBERON:0002129	70.41	gold quality
right hemisphere of cerebellum	UBERON:0014890	69.82	gold quality
cerebellum	UBERON:0002037	69.73	gold quality
ganglionic eminence	UBERON:0004023	69.31	gold quality
middle temporal gyrus	UBERON:0002771	68.37	gold quality
cardiac muscle of right atrium	UBERON:0003379	68.35	gold quality
left ventricle myocardium	UBERON:0006566	68.07	gold quality
prefrontal cortex	UBERON:0000451	66.48	gold quality
leukocyte	CL:0000738	66.36	gold quality
primary visual cortex	UBERON:0002436	66.21	gold quality
right testis	UBERON:0004534	65.93	gold quality
monocyte	CL:0000576	65.63	gold quality
sperm	CL:0000019	65.51	gold quality
Brodmann (1909) area 9	UBERON:0013540	64.44	gold quality
left testis	UBERON:0004533	64.27	gold quality
right frontal lobe	UBERON:0002810	63.69	gold quality
testis	UBERON:0000473	63.47	gold quality
mucosa of paranasal sinus	UBERON:0005030	63.38	gold quality
frontal cortex	UBERON:0001870	63.33	gold quality
neocortex	UBERON:0001950	63.10	gold quality
ventricular zone	UBERON:0003053	62.78	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	62.52	gold quality
ileal mucosa	UBERON:0000331	61.51	silver quality
occipital lobe	UBERON:0002021	61.48	gold quality
cerebral cortex	UBERON:0000956	61.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.09

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2599.1	TIGD3

JASPAR matrix evidence (PMIDs): PMID:39605368

miRNA regulators (miRDB)

30 targeting TIGD3, 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-3692-3P	99.98	70.27	2139
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-1236-3P	99.94	68.04	1695
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-6508-5P	99.92	70.67	2465
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-6830-5P	99.01	68.73	1884
HSA-MIR-138-2-3P	98.91	68.33	1643
HSA-MIR-5581-3P	98.55	70.31	1161
HSA-MIR-5088-3P	98.29	66.63	1310
HSA-MIR-561-5P	98.25	68.13	1365
HSA-MIR-3920	97.75	69.02	1168
HSA-MIR-3189-5P	97.55	66.71	655
HSA-MIR-4287	97.55	67.24	1247
HSA-MIR-4685-3P	97.55	67.35	1255

Literature-anchored findings (GeneRIF, showing 1)

• The strongest candidate as CENP-B paralogue, TIGD3, demonstrated no native centromeric binding when using raised antibodies, either in human cells or in cenpb (-/-) mouse ES cells. (PMID:22080934)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tigd3	ENSMUSG00000044390
rattus_norvegicus	Tigd3	ENSRNOG00000023318

Paralogs (12): CENPB (ENSG00000125817), TIGD7 (ENSG00000140993), POGK (ENSG00000143157), POGZ (ENSG00000143442), TIGD6 (ENSG00000164296), TIGD4 (ENSG00000169989), TIGD5 (ENSG00000179886), TIGD2 (ENSG00000180346), JRKL (ENSG00000183340), TIGD1 (ENSG00000221944), JRK (ENSG00000234616), (ENSG00000293642)

Protein

Protein identifiers

Tigger transposable element-derived protein 3 — Q6B0B8 (reviewed: Q6B0B8)

All UniProt accessions (1): Q6B0B8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Similarity. Belongs to the tigger transposable element derived protein family.

RefSeq proteins (1): NP_663771* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004875	DDE_SF_endonuclease_dom	Domain
IPR006600	HTH_CenpB_DNA-bd_dom	Domain
IPR007889	HTH_Psq	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR050863	CenT-Element_Derived	Family

Pfam: PF03184, PF03221, PF04218

UniProt features (6 total): domain 3, DNA-binding region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6B0B8-F1	79.94	0.40

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 61 (showing top): BENPORATH_ES_WITH_H3K27ME3, chr11q13, WTGAAAT_UNKNOWN, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_UP, FIGUEROA_AML_METHYLATION_CLUSTER_1_UP, FIGUEROA_AML_METHYLATION_CLUSTER_2_UP, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, FIGUEROA_AML_METHYLATION_CLUSTER_4_UP, FIGUEROA_AML_METHYLATION_CLUSTER_5_UP, FIGUEROA_AML_METHYLATION_CLUSTER_6_UP, FIGUEROA_AML_METHYLATION_CLUSTER_7_UP, GSE14386_UNTREATED_VS_IFNA_TREATED_ACT_PBMC_MS_PATIENT_UP, ZNF423_TARGET_GENES, MIR548AJ_3P_MIR548X_3P, MIR548AE_3P_MIR548AQ_3P

GO Biological Process (0):

GO Molecular Function (3): DNA binding (GO:0003677), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
nucleic acid binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

296 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TIGD3	FRMD8	Q9BZ67	637
TIGD3	SLC25A45	Q8N413	613
TIGD3	EHBP1L1	Q8N3D4	609
TIGD3	RALYL	Q86SE5	547
TIGD3	FAM89B	Q8N5H3	545
TIGD3	POGK	Q9P215	542
TIGD3	KLHDC8B	Q8IXV7	499
TIGD3	NAIF1	Q69YI7	491
TIGD3	OR52N5	Q8NH56	474
TIGD3	DPF2	Q92785	469
TIGD3	KCNK7	Q9Y2U2	467
TIGD3	CDC42EP2	O14613	447
TIGD3	CENPBD1P	B2RD01	420
TIGD3	TIGD5	Q53EQ6	420
TIGD3	ZNRD2	O60232	399

IntAct

19 interactions, top by confidence:

A	B	Type	Score
RALY	TIGD3	psi-mi:“MI:0915”(physical association)	0.560
TIGD3	RALYL	psi-mi:“MI:0915”(physical association)	0.560
TIGD3	PNMA3	psi-mi:“MI:0915”(physical association)	0.560
TLE5	TIGD3	psi-mi:“MI:0915”(physical association)	0.560
TIGD3	UBE2I	psi-mi:“MI:0915”(physical association)	0.560
TIGD3	CTPS1	psi-mi:“MI:0914”(association)	0.530
TIGD3	ARHGEF11	psi-mi:“MI:0914”(association)	0.350
TIGD3	RALY	psi-mi:“MI:0915”(physical association)	0.000
TIGD3	PNMA3	psi-mi:“MI:0915”(physical association)	0.000
TIGD3	TLE5	psi-mi:“MI:0915”(physical association)	0.000
RALYL	TIGD3	psi-mi:“MI:0915”(physical association)	0.000
TIGD3	UBE2I	psi-mi:“MI:0915”(physical association)	0.000
TIGD3	RALYL	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): CTPS2 (Affinity Capture-MS), DDB2 (Affinity Capture-MS), CTPS1 (Affinity Capture-MS), NAT16 (Affinity Capture-MS), TIGD3 (Two-hybrid), TIGD3 (Two-hybrid), TIGD3 (Two-hybrid), PNMA3 (Two-hybrid), RALYL (Two-hybrid), SELT (Affinity Capture-MS), DDB2 (Affinity Capture-MS), CTPS2 (Affinity Capture-MS), CTPS1 (Affinity Capture-MS), NAT16 (Affinity Capture-MS), ARHGEF11 (Affinity Capture-MS)

ESM2 similar proteins: A0A061IR73, A0A1B0GUU1, A6H687, A8MYJ7, B1WC39, D3ZVB0, E1BD59, G3MY25, G3MZC5, O75064, P07199, P27790, P29597, P48988, P52333, P52824, Q08DF2, Q0VCE3, Q13608, Q1JPD6, Q2VPB7, Q3TAP4, Q3U1Y4, Q3ZBE0, Q499M4, Q53EQ6, Q5JZY3, Q62137, Q63272, Q6B0B8, Q6DI92, Q6ZPS2, Q6ZS72, Q7TM95, Q80VI1, Q86UT6, Q8BYG9, Q8N9M5, Q8R5G7, Q8TE96

Diamond homologs: P07199, P27790, P48988, P49451, Q17RP2, Q4W5G0, Q6B0B8, Q8IY51, Q8BUZ3, Q7TM95, Q6NT04

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

204 predictions. Top by Δscore:

Variant	Effect	Δscore
11:65354954:TGAG:T	donor_loss	0.9900
11:65354955:GAGG:G	donor_loss	0.9900
11:65354956:AG:A	donor_loss	0.9900
11:65354957:GGT:G	donor_loss	0.9900
11:65354959:T:G	donor_loss	0.9900
11:65355788:CACA:C	acceptor_loss	0.9900
11:65355790:CAGG:C	acceptor_loss	0.9900
11:65355791:A:AG	acceptor_gain	0.9800
11:65355792:G:GG	acceptor_gain	0.9800
11:65355792:GGT:G	acceptor_gain	0.9800
11:65355789:ACAG:A	acceptor_gain	0.9700
11:65355786:C:CA	acceptor_gain	0.9600
11:65355789:A:AG	acceptor_gain	0.9600
11:65355790:C:G	acceptor_gain	0.9600
11:65354958:G:GG	donor_gain	0.9400
11:65354956:AGGTG:A	donor_gain	0.9300
11:65355792:GGTGC:G	acceptor_gain	0.9300
11:65354857:T:TA	donor_gain	0.9200
11:65354955:GAG:G	donor_gain	0.9200
11:65355697:C:T	donor_gain	0.9200
11:65355791:AG:A	acceptor_gain	0.9200
11:65355792:GG:G	acceptor_gain	0.9200
11:65355791:AGGT:A	acceptor_gain	0.8800
11:65355792:GGTG:G	acceptor_gain	0.8800
11:65355029:G:T	donor_gain	0.8700
11:65354958:G:A	donor_gain	0.8500
11:65355029:G:GT	donor_gain	0.8400
11:65354957:GGTG:G	donor_gain	0.8300
11:65354910:G:GT	donor_gain	0.8100
11:65354959:T:A	donor_gain	0.8000

AlphaMissense

3027 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:65355912:C:A	A35D	1.000
11:65355920:T:C	F38L	0.999
11:65355922:C:A	F38L	0.999
11:65355922:C:G	F38L	0.999
11:65355927:T:A	V40D	0.999
11:65355942:T:A	I45N	0.999
11:65355942:T:C	I45T	0.999
11:65355942:T:G	I45S	0.999
11:65355948:G:C	R47P	0.999
11:65355859:G:C	K17N	0.998
11:65355859:G:T	K17N	0.998
11:65355911:G:C	A35P	0.998
11:65355920:T:A	F38I	0.998
11:65355921:T:C	F38S	0.998
11:65355951:T:C	I48T	0.998
11:65356016:C:A	R70S	0.998
11:65356175:T:A	W123R	0.998
11:65356175:T:C	W123R	0.998
11:65356187:T:A	W127R	0.998
11:65356187:T:C	W127R	0.998
11:65356188:G:C	W127S	0.998
11:65356189:G:C	W127C	0.998
11:65356189:G:T	W127C	0.998
11:65355876:T:C	L23P	0.997
11:65355901:G:C	Q31H	0.997
11:65355901:G:T	Q31H	0.997
11:65355920:T:G	F38V	0.997
11:65355934:G:C	Q42H	0.997
11:65355934:G:T	Q42H	0.997
11:65355940:G:C	Q44H	0.997

dbSNP variants (sampled 300 via entrez): RS1000392770 (11:65354482 G>C), RS1000446606 (11:65354577 TC>T), RS1001239360 (11:65355626 G>A,C,T), RS1001503323 (11:65354838 G>C), RS1001607208 (11:65355826 G>A,C), RS1001952169 (11:65355075 T>A,C), RS1003508579 (11:65357830 C>T), RS1003537610 (11:65357242 G>C), RS1004030813 (11:65357527 G>C), RS1004897722 (11:65352774 C>T), RS1005110688 (11:65354673 G>A), RS1005578465 (11:65357565 T>C), RS1005894306 (11:65354121 A>G), RS1006113239 (11:65356155 A>G), RS1006145770 (11:65355877 C>T)

Disease associations

OMIM: gene MIM:619084 | 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
GCST002481_8	Acne (severe)	3.000000e-11

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
Tobacco Smoke Pollution	increases expression	2
triphenyl phosphate	affects expression	1
trichostatin A	decreases expression	1
beta-lapachone	decreases expression	1
ferrous chloride	decreases expression	1
CGP 52608	affects binding, increases reaction	1
licochalcone B	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Leflunomide	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Hydrogen Peroxide	affects expression	1
Niclosamide	decreases expression	1
Rotenone	decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Aflatoxin B1	increases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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