GIN1

Summary

GIN1 (gypsy retrotransposon integrase 1, HGNC:25959) is a protein-coding gene on chromosome 5q21.1, encoding Gypsy retrotransposon integrase-like protein 1 (Q9NXP7).

Predicted to enable nucleic acid binding activity. Predicted to be involved in DNA integration.

Source: NCBI Gene 54826 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 80 total
• MANE Select transcript: NM_017676

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25959
Approved symbol	GIN1
Name	gypsy retrotransposon integrase 1
Location	5q21.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20125, GIN-1, TGIN1
Ensembl gene	ENSG00000145723
Ensembl biotype	protein_coding
Entrez	54826

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000399004, ENST00000507478, ENST00000508629, ENST00000511400, ENST00000512248, ENST00000513603, ENST00000513747, ENST00000910330, ENST00000910331, ENST00000910332, ENST00000910333, ENST00000910334, ENST00000926085, ENST00000926086, ENST00000926087

RefSeq mRNA: 2 — MANE Select: NM_017676 NM_001317954, NM_017676

CCDS: CCDS43349

Canonical transcript exons

ENST00000399004 — 8 exons

Exon	Start	End
ENSE00000971862	103106716	103106909
ENSE00001174759	103120064	103120138
ENSE00002028587	103086000	103088172
ENSE00003461986	103096541	103096826
ENSE00003462342	103097590	103097781
ENSE00003479475	103104541	103104846
ENSE00003591106	103097314	103097490
ENSE00003621099	103108569	103108714

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 89.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.6778 / max 200.9506, expressed in 1579 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
62789	5.6778	1579

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.00	gold quality
biceps brachii	UBERON:0001507	86.58	gold quality
diaphragm	UBERON:0001103	86.37	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	85.98	gold quality
buccal mucosa cell	CL:0002336	85.73	gold quality
heart right ventricle	UBERON:0002080	85.57	gold quality
myocardium	UBERON:0002349	82.25	gold quality
deltoid	UBERON:0001476	82.13	gold quality
calcaneal tendon	UBERON:0003701	82.09	gold quality
secondary oocyte	CL:0000655	81.60	gold quality
vastus lateralis	UBERON:0001379	81.30	gold quality
hindlimb stylopod muscle	UBERON:0004252	81.30	gold quality
ventricular zone	UBERON:0003053	81.29	gold quality
esophagus squamous epithelium	UBERON:0006920	81.19	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.16	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	81.13	gold quality
quadriceps femoris	UBERON:0001377	80.99	gold quality
adrenal tissue	UBERON:0018303	80.90	gold quality
germinal epithelium of ovary	UBERON:0001304	80.54	gold quality
skeletal muscle tissue	UBERON:0001134	80.33	gold quality
muscle organ	UBERON:0001630	80.23	gold quality
visceral pleura	UBERON:0002401	80.14	gold quality
epithelium of nasopharynx	UBERON:0001951	80.12	gold quality
muscle tissue	UBERON:0002385	79.87	gold quality
muscle of leg	UBERON:0001383	79.86	gold quality
heart left ventricle	UBERON:0002084	79.82	gold quality
parietal pleura	UBERON:0002400	79.76	gold quality
tibia	UBERON:0000979	79.74	gold quality
cardiac ventricle	UBERON:0002082	79.73	gold quality
hair follicle	UBERON:0002073	79.64	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.44
E-MTAB-6678	no	3.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting GIN1, 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-1277-5P	100.00	73.95	5056
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-652-5P	99.91	67.49	505
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-370-5P	99.78	66.81	706
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-1284	99.67	73.56	1353
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gin1	ENSMUSG00000026333
rattus_norvegicus	Gin1	ENSRNOG00000011962

Protein

Protein identifiers

Gypsy retrotransposon integrase-like protein 1 — Q9NXP7 (reviewed: Q9NXP7)

Alternative names: Ty3/Gypsy integrase 1, Zinc finger H2C2 domain-containing protein

All UniProt accessions (1): Q9NXP7

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Widely expressed. Also found in tumors originating from parathyroid gland, colon, stomach, bladder, uterus and prostate.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NXP7-1	1	yes
Q9NXP7-2	2
Q9NXP7-3	3

RefSeq proteins (2): NP_001304883, NP_060146* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001584	Integrase_cat-core	Domain
IPR012337	RNaseH-like_sf	Homologous_superfamily
IPR036397	RNaseH_sf	Homologous_superfamily
IPR041588	Integrase_H2C2	Domain
IPR050951

Pfam: PF00665, PF17921

UniProt features (11 total): splice variant 4, sequence conflict 2, sequence variant 2, chain 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NXP7-F1	70.95	0.30

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 (1): 502

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_DNA_INTEGRATION, MODULE_205, GGAANCGGAANY_UNKNOWN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, chr5q21, GOBP_DNA_METABOLIC_PROCESS, SIRNA_EIF4GI_UP, SHEN_SMARCA2_TARGETS_UP, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GSE5503_PLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, ALKBH3_TARGET_GENES, BARX1_TARGET_GENES, DIDO1_TARGET_GENES

GO Biological Process (1): DNA integration (GO:0015074)

GO Molecular Function (1): nucleic acid binding (GO:0003676)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA metabolic process	1
binding	1

Protein interactions and networks

STRING

740 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GIN1	KRABD2	Q6ZNG9	664
GIN1	PGBD5	Q8N414	659
GIN1	HARBI1	Q96MB7	592
GIN1	FAM110B	Q8TC76	549
GIN1	MACIR	Q96GV9	542
GIN1	THAP9	Q9H5L6	531
GIN1	BUD31	P41223	521
GIN1	DRC8	Q5VUJ9	507
GIN1	DHX8	Q14562	501
GIN1	UBXN8	O00124	497
GIN1	CGGBP1	Q9UFW8	492
GIN1	SUGP2	Q8IX01	492
GIN1	AKR1B15	C9JRZ8	481
GIN1	PGBD1	Q96JS3	477
GIN1	ZBED8	Q8IZ13	477

IntAct

4 interactions, top by confidence:

A	B	Type	Score
GIN1	GSTA2	psi-mi:“MI:0915”(physical association)	0.400
CPSF6	GIN1	psi-mi:“MI:0915”(physical association)	0.370
	GIN1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (15): GIN1 (Two-hybrid), GIN1 (Affinity Capture-MS), GIN1 (Two-hybrid), GIN1 (Affinity Capture-MS), GIN1 (Affinity Capture-RNA), GSTA2 (Affinity Capture-MS), GIN1 (Affinity Capture-MS), RPS14 (Cross-Linking-MS (XL-MS)), RPS14 (Cross-Linking-MS (XL-MS)), RPS28 (Cross-Linking-MS (XL-MS)), RPS19 (Cross-Linking-MS (XL-MS)), GIN1 (Cross-Linking-MS (XL-MS)), GIN1 (Cross-Linking-MS (XL-MS)), GIN1 (Cross-Linking-MS (XL-MS)), GIN1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B7P3V8, A4FUB7, A4H7G5, A4HVU6, A6NKG5, B4NSS9, B6EU02, F4I1N8, H2KZW3, O10318, O13329, P04586, P0C2J7, P18475, P34601, P47024, Q01577, Q05101, Q09178, Q09293, Q1L6Q1, Q3S4A7, Q4DCH3, Q4QFY1, Q4R6I1, Q52QI2, Q57X81, Q5RBK0, Q5RDX4, Q62120, Q66H30, Q6R2W3, Q7KLI1, Q7LHG5, Q8CDM1, Q8K259, Q8N157, Q90179, Q91829, Q99315

Diamond homologs: A4FUB7, Q4R6I1, Q5RBK0, Q66H30, Q8K259, Q9NXP7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	65
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1408 predictions. Top by Δscore:

Variant	Effect	Δscore
5:103088169:CTTT:C	acceptor_gain	1.0000
5:103088170:TTT:T	acceptor_gain	1.0000
5:103088173:C:CC	acceptor_gain	1.0000
5:103097588:A:AC	donor_gain	1.0000
5:103097588:A:C	donor_loss	1.0000
5:103097589:C:CC	donor_gain	1.0000
5:103106715:CCCA:C	donor_gain	1.0000
5:103106718:A:AC	donor_gain	1.0000
5:103106719:C:CC	donor_gain	1.0000
5:103108563:TTTTA:T	donor_loss	1.0000
5:103108564:TTTA:T	donor_loss	1.0000
5:103108565:TTACC:T	donor_loss	1.0000
5:103108566:TAC:T	donor_loss	1.0000
5:103108567:A:AT	donor_loss	1.0000
5:103108568:CCTT:C	donor_loss	1.0000
5:103088153:T:C	acceptor_gain	0.9900
5:103088170:TTTC:T	acceptor_loss	0.9900
5:103088171:TT:T	acceptor_gain	0.9900
5:103088172:TCTGA:T	acceptor_loss	0.9900
5:103088173:C:CA	acceptor_loss	0.9900
5:103096833:G:GC	acceptor_gain	0.9900
5:103097453:C:CC	acceptor_gain	0.9900
5:103097589:CCAA:C	donor_gain	0.9900
5:103097777:TTGAT:T	acceptor_gain	0.9900
5:103097778:TGAT:T	acceptor_gain	0.9900
5:103097781:TCTGA:T	acceptor_loss	0.9900
5:103097782:C:CC	acceptor_gain	0.9900
5:103097782:C:T	acceptor_loss	0.9900
5:103097783:T:A	acceptor_loss	0.9900
5:103106707:AAG:A	donor_gain	0.9900

AlphaMissense

3479 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:103096573:A:G	L421P	0.999
5:103096657:A:T	I393K	0.999
5:103106726:A:T	V108D	0.999
5:103106748:A:G	W101R	0.999
5:103106748:A:T	W101R	0.999
5:103108579:A:C	F43L	0.999
5:103108579:A:T	F43L	0.999
5:103108581:A:G	F43L	0.999
5:103108590:C:G	A40P	0.999
5:103108656:A:C	Y18D	0.999
5:103096573:A:T	L421H	0.998
5:103096719:T:A	R372S	0.998
5:103096719:T:G	R372S	0.998
5:103096726:A:T	V370D	0.998
5:103106751:A:C	Y100D	0.998
5:103106774:A:G	L92P	0.998
5:103108580:A:G	F43S	0.998
5:103108601:A:C	I36R	0.998
5:103108601:A:T	I36K	0.998
5:103096624:A:G	L404P	0.997
5:103096630:G:T	A402D	0.997
5:103096657:A:C	I393R	0.997
5:103104837:A:G	C115R	0.997
5:103106746:C:A	W101C	0.997
5:103106746:C:G	W101C	0.997
5:103108589:G:T	A40E	0.997
5:103108593:C:G	A39P	0.997
5:103108594:T:A	R38S	0.997
5:103108594:T:G	R38S	0.997
5:103108597:T:A	R37S	0.997

dbSNP variants (sampled 300 via entrez): RS1000354781 (5:103091242 T>C), RS1000366570 (5:103097180 T>C), RS1000574460 (5:103115767 A>C), RS1000707441 (5:103110206 A>G), RS1000861992 (5:103086067 A>G), RS1000918419 (5:103092263 T>C), RS1000983868 (5:103121515 C>G), RS1000999178 (5:103092632 C>G,T), RS1001014865 (5:103121862 A>G), RS1001240864 (5:103113330 T>C), RS1001566269 (5:103113027 G>A), RS1001627608 (5:103089785 C>A,T), RS1001649089 (5:103118712 T>C), RS1001680344 (5:103119089 T>C), RS1001994887 (5:103089517 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

8 associations (top):

Study	Trait	p-value
GCST003129_2	Primary biliary cholangitis	1.000000e-08
GCST005568_19	Rheumatoid arthritis (ACPA-positive)	3.000000e-06
GCST005568_33	Rheumatoid arthritis (ACPA-positive)	9.000000e-08
GCST005569_41	Rheumatoid arthritis	9.000000e-08
GCST005569_8	Rheumatoid arthritis	7.000000e-10
GCST007559_21	Sleep duration (short sleep)	2.000000e-08
GCST010002_34	Refractive error	2.000000e-10
GCST90000025_2	Appendicular lean mass	1.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases abundance	2
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
resorcinol	decreases expression	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
jinfukang	decreases expression	1
Vorinostat	increases expression	1
Cisplatin	decreases expression	1
Formaldehyde	decreases expression	1
Smoke	decreases expression, increases abundance	1
Thimerosal	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin M1	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases abundance, decreases expression	1

Clinical trials (associated diseases)

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