GIN1 (gypsy retrotransposon integrase 1) - Rat Genome Database

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Gene: GIN1 (gypsy retrotransposon integrase 1) Homo sapiens
Analyze
Symbol: GIN1
Name: gypsy retrotransposon integrase 1
RGD ID: 1603218
HGNC Page HGNC:25959
Description: Predicted to enable nucleic acid binding activity. Predicted to be involved in DNA integration.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: FLJ20125; GIN-1; gypsy integrase 1; gypsy retrotransposon integrase-like protein 1; TGIN1; Ty3/Gypsy integrase 1; ZH2C2; zinc finger H2C2 domain-containing protein; zinc finger, H2C2 domain containing
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385103,086,000 - 103,120,138 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5103,086,000 - 103,120,138 (-)EnsemblGRCh38hg38GRCh38
GRCh375102,421,704 - 102,455,842 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365102,449,603 - 102,483,741 (-)NCBINCBI36Build 36hg18NCBI36
Celera598,369,538 - 98,403,680 (-)NCBICelera
Cytogenetic Map5q21.1NCBI
HuRef597,602,973 - 97,637,114 (-)NCBIHuRef
CHM1_15101,854,334 - 101,888,476 (-)NCBICHM1_1
T2T-CHM13v2.05103,594,035 - 103,628,240 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8125298   PMID:11470852   PMID:12477932   PMID:16189514   PMID:16344560   PMID:20379614   PMID:24623722   PMID:25925205   PMID:32235678   PMID:32393512   PMID:33961781   PMID:35256949  


Genomics

Comparative Map Data
GIN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385103,086,000 - 103,120,138 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5103,086,000 - 103,120,138 (-)EnsemblGRCh38hg38GRCh38
GRCh375102,421,704 - 102,455,842 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365102,449,603 - 102,483,741 (-)NCBINCBI36Build 36hg18NCBI36
Celera598,369,538 - 98,403,680 (-)NCBICelera
Cytogenetic Map5q21.1NCBI
HuRef597,602,973 - 97,637,114 (-)NCBIHuRef
CHM1_15101,854,334 - 101,888,476 (-)NCBICHM1_1
T2T-CHM13v2.05103,594,035 - 103,628,240 (-)NCBIT2T-CHM13v2.0
Gin1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39197,697,894 - 97,721,435 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl197,697,897 - 97,721,434 (+)EnsemblGRCm39 Ensembl
GRCm38197,770,172 - 97,793,710 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl197,770,172 - 97,793,709 (+)EnsemblGRCm38mm10GRCm38
MGSCv37199,666,756 - 99,689,548 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36199,600,606 - 99,623,375 (+)NCBIMGSCv36mm8
Celera1100,649,677 - 100,673,455 (+)NCBICelera
Cytogenetic Map1DNCBI
cM Map147.76NCBI
Gin1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89105,740,914 - 105,762,357 (-)NCBIGRCr8
mRatBN7.2998,293,596 - 98,315,155 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl998,293,597 - 98,315,848 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9106,708,493 - 106,728,718 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09111,836,476 - 111,856,701 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09110,179,867 - 110,200,092 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09111,200,285 - 111,220,738 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9111,199,141 - 111,220,693 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09110,750,567 - 110,770,987 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4997,070,918 - 97,091,577 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1997,280,493 - 97,293,502 (-)NCBI
Celera995,736,354 - 95,756,618 (-)NCBICelera
Cytogenetic Map9q36NCBI
Gin1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541810,898,293 - 10,918,544 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541810,898,069 - 10,918,460 (+)NCBIChiLan1.0ChiLan1.0
GIN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2498,363,395 - 98,404,407 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1596,364,376 - 96,690,507 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0598,440,271 - 98,475,300 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15104,143,456 - 104,175,826 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5104,124,849 - 104,175,826 (-)Ensemblpanpan1.1panPan2
GIN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.138,088,719 - 8,116,461 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl38,088,515 - 8,116,436 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha39,490,244 - 9,518,001 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.037,976,941 - 8,004,710 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl37,977,034 - 8,004,701 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.137,917,409 - 7,945,154 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.037,936,158 - 7,964,988 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.038,095,976 - 8,123,752 (+)NCBIUU_Cfam_GSD_1.0
Gin1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213163,232,989 - 163,258,059 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365231,418,316 - 1,443,618 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365231,418,387 - 1,443,322 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GIN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2108,561,387 - 108,597,262 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12108,561,132 - 108,599,017 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22112,579,162 - 112,614,955 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GIN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1236,528,728 - 6,562,314 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl236,526,425 - 6,563,044 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660367,766,036 - 7,801,636 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gin1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474321,212,688 - 21,236,882 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in GIN1
25 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q13.3-22.1(chr5:74163186-110809453)x3 copy number gain See cases [RCV000051839] Chr5:74163186..110809453 [GRCh38]
Chr5:73459011..110145153 [GRCh37]
Chr5:73494767..110173052 [NCBI36]
Chr5:5q13.3-22.1		 pathogenic
GRCh38/hg38 5q15-22.3(chr5:96454445-114050905)x3 copy number gain See cases [RCV000051841] Chr5:96454445..114050905 [GRCh38]
Chr5:95790149..113386602 [GRCh37]
Chr5:95815905..113414501 [NCBI36]
Chr5:5q15-22.3		 pathogenic
GRCh38/hg38 5q14.3-21.2(chr5:89081352-104687248)x1 copy number loss See cases [RCV000053516] Chr5:89081352..104687248 [GRCh38]
Chr5:88377169..104022949 [GRCh37]
Chr5:88412925..104050848 [NCBI36]
Chr5:5q14.3-21.2		 pathogenic
GRCh38/hg38 5q21.1-22.2(chr5:102373396-113594030)x1 copy number loss See cases [RCV000053523] Chr5:102373396..113594030 [GRCh38]
Chr5:101709100..112929727 [GRCh37]
Chr5:101736999..112957626 [NCBI36]
Chr5:5q21.1-22.2		 pathogenic
NM_017676.2(GIN1):c.431C>T (p.Thr144Ile) single nucleotide variant Malignant melanoma [RCV000061080] Chr5:103104749 [GRCh38]
Chr5:102440453 [GRCh37]
Chr5:102468352 [NCBI36]
Chr5:5q21.1		 not provided
GRCh38/hg38 5q21.1-21.2(chr5:102812129-104230720)x3 copy number gain See cases [RCV000138667] Chr5:102812129..104230720 [GRCh38]
Chr5:102147833..103566421 [GRCh37]
Chr5:102175732..103594320 [NCBI36]
Chr5:5q21.1-21.2		 likely benign
GRCh38/hg38 5q14.3-23.3(chr5:90374606-128076423)x1 copy number loss See cases [RCV000139893] Chr5:90374606..128076423 [GRCh38]
Chr5:89670423..127412115 [GRCh37]
Chr5:89706179..127440014 [NCBI36]
Chr5:5q14.3-23.3		 pathogenic
GRCh38/hg38 5q14.3-22.1(chr5:84603580-111435081)x1 copy number loss See cases [RCV000139656] Chr5:84603580..111435081 [GRCh38]
Chr5:83899398..110770779 [GRCh37]
Chr5:83935154..110798678 [NCBI36]
Chr5:5q14.3-22.1		 pathogenic
GRCh38/hg38 5q14.3-23.1(chr5:92899734-119614119)x1 copy number loss See cases [RCV000141252] Chr5:92899734..119614119 [GRCh38]
Chr5:92235441..118949814 [GRCh37]
Chr5:92261197..118977713 [NCBI36]
Chr5:5q14.3-23.1		 pathogenic
GRCh38/hg38 5q15-22.2(chr5:93193104-113287795)x1 copy number loss See cases [RCV000143249] Chr5:93193104..113287795 [GRCh38]
Chr5:92528810..112623492 [GRCh37]
Chr5:92554566..112651391 [NCBI36]
Chr5:5q15-22.2		 pathogenic
GRCh38/hg38 5q14.3-31.1(chr5:91411708-131319563)x1 copy number loss See cases [RCV000143746] Chr5:91411708..131319563 [GRCh38]
Chr5:90707525..130655256 [GRCh37]
Chr5:90743281..130683155 [NCBI36]
Chr5:5q14.3-31.1		 pathogenic
GRCh37/hg19 5q15-35.3(chr5:94844077-178830410)x3 copy number gain not provided [RCV000487658] Chr5:94844077..178830410 [GRCh37]
Chr5:5q15-35.3		 likely benign
GRCh37/hg19 5q21.1-23.2(chr5:100607918-125900735)x1 copy number loss See cases [RCV000445968] Chr5:100607918..125900735 [GRCh37]
Chr5:5q21.1-23.2		 pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789) copy number gain See cases [RCV000510723] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3		 pathogenic
GRCh37/hg19 5q15-21.2(chr5:95049966-103537589)x1 copy number loss See cases [RCV000510548] Chr5:95049966..103537589 [GRCh37]
Chr5:5q15-21.2		 likely pathogenic
GRCh37/hg19 5p15.1-q35.2(chr5:17628741-176575720)x1 copy number loss See cases [RCV000511978] Chr5:17628741..176575720 [GRCh37]
Chr5:5p15.1-q35.2		 pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)x3 copy number gain See cases [RCV000512039] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3		 pathogenic
GRCh37/hg19 5q21.1-21.2(chr5:98845559-103355831)x1 copy number loss See cases [RCV000511250] Chr5:98845559..103355831 [GRCh37]
Chr5:5q21.1-21.2		 uncertain significance
NC_000005.9:g.(?_86400000)_(154000000_?)del deletion Familial adenomatous polyposis 1 [RCV002231249]|Hereditary cancer-predisposing syndrome [RCV000554476] Chr5:86400000..154000000 [GRCh37]
Chr5:5q14.3-33.2		 pathogenic
GRCh37/hg19 5q21.1(chr5:102398221-102788681)x3 copy number gain not provided [RCV000682586] Chr5:102398221..102788681 [GRCh37]
Chr5:5q21.1		 likely benign
GRCh37/hg19 5q14.3-21.3(chr5:91504101-104858348)x1 copy number loss not provided [RCV000682580] Chr5:91504101..104858348 [GRCh37]
Chr5:5q14.3-21.3		 pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:25328-180693344)x3 copy number gain not provided [RCV000744323] Chr5:25328..180693344 [GRCh37]
Chr5:5p15.33-q35.3		 pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:13648-180905029)x3 copy number gain not provided [RCV000744317] Chr5:13648..180905029 [GRCh37]
Chr5:5p15.33-q35.3		 pathogenic
Single allele deletion Neurodevelopmental disorder [RCV000787436] Chr5:14685137..149511942 [GRCh37]
Chr5:5p15.2-q32		 uncertain significance
GRCh37/hg19 5q14.3-23.3(chr5:89949118-129317455)x3 copy number gain not provided [RCV000849289] Chr5:89949118..129317455 [GRCh37]
Chr5:5q14.3-23.3		 pathogenic
GRCh37/hg19 5q21.1(chr5:102096690-102460794)x1 copy number loss not provided [RCV000846950] Chr5:102096690..102460794 [GRCh37]
Chr5:5q21.1		 uncertain significance
GRCh37/hg19 5q21.1-21.2(chr5:102422529-104039584)x3 copy number gain not provided [RCV000849385] Chr5:102422529..104039584 [GRCh37]
Chr5:5q21.1-21.2		 uncertain significance
GRCh37/hg19 5q21.1-21.2(chr5:101152187-103638623)x3 copy number gain not provided [RCV001005707] Chr5:101152187..103638623 [GRCh37]
Chr5:5q21.1-21.2		 uncertain significance
GRCh37/hg19 5q21.1(chr5:101620402-102584810)x3 copy number gain not provided [RCV001005708] Chr5:101620402..102584810 [GRCh37]
Chr5:5q21.1		 likely benign
NM_017676.2(GIN1):c.716C>T (p.Thr239Met) single nucleotide variant not provided [RCV001671382] Chr5:103097705 [GRCh38]
Chr5:102433409 [GRCh37]
Chr5:5q21.1		 benign
GRCh37/hg19 5q14.3-21.3(chr5:87792844-109221844)x3 copy number gain See cases [RCV001007415] Chr5:87792844..109221844 [GRCh37]
Chr5:5q14.3-21.3		 likely pathogenic
GRCh37/hg19 5q21.1(chr5:102034608-102540865)x3 copy number gain not provided [RCV001259347] Chr5:102034608..102540865 [GRCh37]
Chr5:5q21.1		 uncertain significance
GRCh37/hg19 5q21.1(chr5:102096690-102460794)x1 copy number loss not provided [RCV001259346] Chr5:102096690..102460794 [GRCh37]
Chr5:5q21.1		 uncertain significance
GRCh37/hg19 5q21.1-23.2(chr5:100607918-125900735) copy number loss not specified [RCV002053515] Chr5:100607918..125900735 [GRCh37]
Chr5:5q21.1-23.2		 pathogenic
GRCh37/hg19 5q15-22.3(chr5:93650000-114969108) copy number loss not specified [RCV002053511] Chr5:93650000..114969108 [GRCh37]
Chr5:5q15-22.3		 pathogenic
NM_017676.2(GIN1):c.1196G>C (p.Ser399Thr) single nucleotide variant Inborn genetic diseases [RCV002777033] Chr5:103096639 [GRCh38]
Chr5:102432343 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.1316G>T (p.Gly439Val) single nucleotide variant Inborn genetic diseases [RCV002869017] Chr5:103088151 [GRCh38]
Chr5:102423855 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.1343T>C (p.Ile448Thr) single nucleotide variant Inborn genetic diseases [RCV002978234] Chr5:103088124 [GRCh38]
Chr5:102423828 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.1342A>G (p.Ile448Val) single nucleotide variant Inborn genetic diseases [RCV002744466] Chr5:103088125 [GRCh38]
Chr5:102423829 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.1247T>C (p.Ile416Thr) single nucleotide variant Inborn genetic diseases [RCV002744947] Chr5:103096588 [GRCh38]
Chr5:102432292 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.88C>T (p.Pro30Ser) single nucleotide variant Inborn genetic diseases [RCV002896977] Chr5:103108620 [GRCh38]
Chr5:102444324 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.69A>T (p.Glu23Asp) single nucleotide variant Inborn genetic diseases [RCV002719629] Chr5:103108639 [GRCh38]
Chr5:102444343 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.1121G>C (p.Arg374Thr) single nucleotide variant Inborn genetic diseases [RCV002809402] Chr5:103096714 [GRCh38]
Chr5:102432418 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.914T>G (p.Val305Gly) single nucleotide variant Inborn genetic diseases [RCV003010597] Chr5:103097408 [GRCh38]
Chr5:102433112 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.662T>G (p.Leu221Trp) single nucleotide variant Inborn genetic diseases [RCV003202403] Chr5:103097759 [GRCh38]
Chr5:102433463 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.404A>G (p.Lys135Arg) single nucleotide variant Inborn genetic diseases [RCV003189547] Chr5:103104776 [GRCh38]
Chr5:102440480 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.379G>A (p.Val127Ile) single nucleotide variant Inborn genetic diseases [RCV003174973] Chr5:103104801 [GRCh38]
Chr5:102440505 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.389A>T (p.Lys130Ile) single nucleotide variant Inborn genetic diseases [RCV003177937] Chr5:103104791 [GRCh38]
Chr5:102440495 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.1301T>A (p.Leu434His) single nucleotide variant Inborn genetic diseases [RCV003287408] Chr5:103088166 [GRCh38]
Chr5:102423870 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.1454T>C (p.Leu485Pro) single nucleotide variant Inborn genetic diseases [RCV003358559] Chr5:103088013 [GRCh38]
Chr5:102423717 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.32A>G (p.His11Arg) single nucleotide variant Inborn genetic diseases [RCV003345639] Chr5:103108676 [GRCh38]
Chr5:102444380 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.525G>T (p.Leu175Phe) single nucleotide variant Inborn genetic diseases [RCV003350576] Chr5:103104655 [GRCh38]
Chr5:102440359 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.727C>A (p.Pro243Thr) single nucleotide variant Inborn genetic diseases [RCV003347356] Chr5:103097694 [GRCh38]
Chr5:102433398 [GRCh37]
Chr5:5q21.1		 uncertain significance
NM_017676.2(GIN1):c.1022A>G (p.Asn341Ser) single nucleotide variant Inborn genetic diseases [RCV003362346] Chr5:103096813 [GRCh38]
Chr5:102432517 [GRCh37]
Chr5:5q21.1		 uncertain significance
GRCh37/hg19 5q15-23.2(chr5:93828571-123711334)x1 copy number loss not specified [RCV003986577] Chr5:93828571..123711334 [GRCh37]
Chr5:5q15-23.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1612
Count of miRNA genes:667
Interacting mature miRNAs:746
Transcripts:ENST00000399004, ENST00000507478, ENST00000508629, ENST00000511400, ENST00000512248, ENST00000513603, ENST00000513747
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
STS-H23482  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375102,423,619 - 102,423,810UniSTSGRCh37
Build 365102,451,518 - 102,451,709RGDNCBI36
Celera598,371,453 - 98,371,644RGD
Cytogenetic Map5q21.1UniSTS
HuRef597,604,888 - 97,605,079UniSTS
GeneMap99-GB4 RH Map5437.05UniSTS
SGC30489  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375102,421,731 - 102,421,830UniSTSGRCh37
Build 365102,449,630 - 102,449,729RGDNCBI36
Celera598,369,565 - 98,369,664RGD
Cytogenetic Map5q21.1UniSTS
HuRef597,603,000 - 97,603,099UniSTS
GeneMap99-GB4 RH Map5442.5UniSTS
Whitehead-RH Map5343.2UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 8 3 6 12 11 4 45 23 81 9 2 1 4
Low 2427 2582 1716 621 1580 462 4323 2142 3682 394 1379 1600 173 1201 2777 5 2
Below cutoff 4 404 4 3 353 3 23 51 7 2 4 3 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001317954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_017676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_134299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005272028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017009599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024446123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047417343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054352864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054352865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC008447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK000132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK225572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK295796 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC015325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC151135 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC157835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR627424 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB101499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000399004   ⟹   ENSP00000381970
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5103,086,000 - 103,120,138 (-)Ensembl
RefSeq Acc Id: ENST00000507478
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5103,087,815 - 103,097,693 (-)Ensembl
RefSeq Acc Id: ENST00000508629   ⟹   ENSP00000427162
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5103,087,813 - 103,120,097 (-)Ensembl
RefSeq Acc Id: ENST00000511400
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5103,102,276 - 103,104,621 (-)Ensembl
RefSeq Acc Id: ENST00000512248   ⟹   ENSP00000422960
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5103,086,000 - 103,120,108 (-)Ensembl
RefSeq Acc Id: ENST00000513603
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5103,106,564 - 103,120,138 (-)Ensembl
RefSeq Acc Id: ENST00000513747   ⟹   ENSP00000423031
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5103,088,126 - 103,120,089 (-)Ensembl
RefSeq Acc Id: NM_001317954   ⟹   NP_001304883
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385103,086,000 - 103,120,138 (-)NCBI
CHM1_15101,854,334 - 101,888,476 (-)NCBI
T2T-CHM13v2.05103,594,035 - 103,628,240 (-)NCBI
Sequence:
RefSeq Acc Id: NM_017676   ⟹   NP_060146
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385103,086,000 - 103,120,138 (-)NCBI
GRCh375102,421,704 - 102,455,842 (-)RGD
Build 365102,449,603 - 102,483,741 (-)NCBI Archive
Celera598,369,538 - 98,403,680 (-)RGD
HuRef597,602,973 - 97,637,114 (-)ENTREZGENE
CHM1_15101,854,334 - 101,888,476 (-)NCBI
T2T-CHM13v2.05103,594,035 - 103,628,240 (-)NCBI
Sequence:
RefSeq Acc Id: NR_134299
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385103,086,000 - 103,120,138 (-)NCBI
CHM1_15101,854,334 - 101,888,476 (-)NCBI
T2T-CHM13v2.05103,594,035 - 103,628,240 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017009599   ⟹   XP_016865088
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385103,086,000 - 103,120,138 (-)NCBI
Sequence:
RefSeq Acc Id: XM_047417343   ⟹   XP_047273299
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385103,086,000 - 103,106,806 (-)NCBI
RefSeq Acc Id: XM_054352864   ⟹   XP_054208839
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.05103,594,035 - 103,626,812 (-)NCBI
RefSeq Acc Id: XM_054352865   ⟹   XP_054208840
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.05103,594,035 - 103,614,836 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_060146   ⟸   NM_017676
- Peptide Label: isoform 1
- UniProtKB: Q6AI03 (UniProtKB/Swiss-Prot),   B4DIV4 (UniProtKB/Swiss-Prot),   B2RXF7 (UniProtKB/Swiss-Prot),   Q96BR2 (UniProtKB/Swiss-Prot),   Q9NXP7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001304883   ⟸   NM_001317954
- Peptide Label: isoform 2
- UniProtKB: Q9NXP7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_016865088   ⟸   XM_017009599
- Peptide Label: isoform X1
- UniProtKB: Q6AI03 (UniProtKB/Swiss-Prot),   B4DIV4 (UniProtKB/Swiss-Prot),   B2RXF7 (UniProtKB/Swiss-Prot),   Q96BR2 (UniProtKB/Swiss-Prot),   Q9NXP7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000381970   ⟸   ENST00000399004
RefSeq Acc Id: ENSP00000427162   ⟸   ENST00000508629
RefSeq Acc Id: ENSP00000422960   ⟸   ENST00000512248
RefSeq Acc Id: ENSP00000423031   ⟸   ENST00000513747
RefSeq Acc Id: XP_047273299   ⟸   XM_047417343
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054208839   ⟸   XM_054352864
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054208840   ⟸   XM_054352865
- Peptide Label: isoform X2
Protein Domains
Integrase catalytic

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9NXP7-F1-model_v2 AlphaFold Q9NXP7 1-522 view protein structure

Promoters
RGD ID:6803091
Promoter ID:HG_KWN:50765
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000274384,   ENST00000321521,   NM_017676,   UC003KOB.1,   UC003KOC.1,   UC003KOD.2,   UC010JBO.1
Position:
Human AssemblyChrPosition (strand)Source
Build 365102,483,456 - 102,484,027 (-)MPROMDB
RGD ID:6870196
Promoter ID:EPDNEW_H8263
Type:initiation region
Name:GIN1_1
Description:gypsy retrotransposon integrase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H8264  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh385103,120,138 - 103,120,198EPDNEW
RGD ID:6870198
Promoter ID:EPDNEW_H8264
Type:multiple initiation site
Name:GIN1_2
Description:gypsy retrotransposon integrase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H8263  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh385103,120,256 - 103,120,316EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:25959 AgrOrtholog
COSMIC GIN1 COSMIC
Ensembl Genes ENSG00000145723 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000399004 ENTREZGENE
  ENST00000399004.7 UniProtKB/Swiss-Prot
  ENST00000508629.5 UniProtKB/Swiss-Prot
  ENST00000512248.5 UniProtKB/Swiss-Prot
  ENST00000513747.1 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.340.70 UniProtKB/Swiss-Prot
  3.30.420.10 UniProtKB/Swiss-Prot
GTEx ENSG00000145723 GTEx
HGNC ID HGNC:25959 ENTREZGENE
Human Proteome Map GIN1 Human Proteome Map
InterPro Integrase_cat-core UniProtKB/Swiss-Prot
  Integrase_H2C2 UniProtKB/Swiss-Prot
  RNaseH-like_sf UniProtKB/Swiss-Prot
  RNaseH_sf UniProtKB/Swiss-Prot
KEGG Report hsa:54826 UniProtKB/Swiss-Prot
NCBI Gene 54826 ENTREZGENE
PANTHER ENDONUCLEASE-RELATED UniProtKB/Swiss-Prot
  GYPSY RETROTRANSPOSON INTEGRASE-LIKE PROTEIN 1 UniProtKB/Swiss-Prot
Pfam Integrase_H2C2 UniProtKB/Swiss-Prot
  rve UniProtKB/Swiss-Prot
PharmGKB PA162389674 PharmGKB
PROSITE INTEGRASE UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53098 UniProtKB/Swiss-Prot
UniProt B2RXF7 ENTREZGENE
  B4DIV4 ENTREZGENE
  GIN1_HUMAN UniProtKB/Swiss-Prot
  Q6AI03 ENTREZGENE
  Q96BR2 ENTREZGENE
  Q9NXP7 ENTREZGENE
UniProt Secondary B2RXF7 UniProtKB/Swiss-Prot
  B4DIV4 UniProtKB/Swiss-Prot
  Q6AI03 UniProtKB/Swiss-Prot
  Q96BR2 UniProtKB/Swiss-Prot