Gin1 (gypsy retrotransposon integrase 1) - Rat Genome Database

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Gene: Gin1 (gypsy retrotransposon integrase 1) Rattus norvegicus
Analyze
Symbol: Gin1
Name: gypsy retrotransposon integrase 1
RGD ID: 1307449
Description: Predicted to enable nucleic acid binding activity. Predicted to be involved in DNA integration. Orthologous to human GIN1 (gypsy retrotransposon integrase 1); INTERACTS WITH 4,4'-diaminodiphenylmethane; atrazine; azoxystrobin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: GIN-1; gypsy retrotransposon integrase-like protein 1; LOC316687; RGD1307449; similar to RIKEN cDNA 4930429M06Rik
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data
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
(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
(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
72 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:73
Interacting mature miRNAs:74
Transcripts:ENSRNOT00000016028
Prediction methods:Microtar, Miranda
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)992491589100929786Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat

Markers in Region
RH143019  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2998,314,374 - 98,314,520 (+)MAPPERmRatBN7.2
Rnor_6.09111,219,984 - 111,220,129NCBIRnor6.0
Rnor_5.09110,770,234 - 110,770,379UniSTSRnor5.0
RGSC_v3.4997,090,910 - 97,091,055UniSTSRGSC3.4
Celera995,755,951 - 95,756,096UniSTS
RH 3.4 Map9818.49UniSTS
Cytogenetic Map9q36UniSTS
AW532587  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2998,317,204 - 98,317,362 (+)MAPPERmRatBN7.2
Rnor_6.09111,222,813 - 111,222,970NCBIRnor6.0
Rnor_5.09110,773,063 - 110,773,220UniSTSRnor5.0
RGSC_v3.4997,093,739 - 97,093,896UniSTSRGSC3.4
Celera995,758,343 - 95,758,500UniSTS
RH 3.4 Map9818.49UniSTS
Cytogenetic Map9q36UniSTS


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 appendage
High
Medium 12 4 7 4 6 6 29 1
Low 3 43 45 37 12 37 8 11 68 29 12 10 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000016028   ⟹   ENSRNOP00000016028
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl998,294,776 - 98,315,042 (-)Ensembl
Rnor_6.0 Ensembl9111,200,383 - 111,220,651 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076441
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9111,218,699 - 111,220,693 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077052
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9111,206,795 - 111,209,286 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087355   ⟹   ENSRNOP00000073007
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl998,293,597 - 98,315,848 (-)Ensembl
Rnor_6.0 Ensembl9111,199,141 - 111,213,098 (-)Ensembl
RefSeq Acc Id: NM_001025012   ⟹   NP_001020183
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89105,742,089 - 105,762,357 (-)NCBI
mRatBN7.2998,294,771 - 98,315,042 (-)NCBI
Rnor_6.09111,200,383 - 111,220,651 (-)NCBI
Rnor_5.09110,750,567 - 110,770,987 (-)NCBI
RGSC_v3.4997,070,918 - 97,091,577 (-)RGD
Celera995,736,354 - 95,756,618 (-)RGD
Sequence:
RefSeq Acc Id: XM_039083782   ⟹   XP_038939710
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89105,740,914 - 105,757,837 (-)NCBI
mRatBN7.2998,293,596 - 98,313,538 (-)NCBI
RefSeq Acc Id: XM_039083784   ⟹   XP_038939712
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89105,740,914 - 105,752,654 (-)NCBI
mRatBN7.2998,293,596 - 98,305,361 (-)NCBI
RefSeq Acc Id: XM_039083785   ⟹   XP_038939713
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89105,740,914 - 105,752,737 (-)NCBI
mRatBN7.2998,293,596 - 98,305,422 (-)NCBI
RefSeq Acc Id: XM_063267333   ⟹   XP_063123403
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89105,740,914 - 105,754,794 (-)NCBI
RefSeq Acc Id: NP_001020183   ⟸   NM_001025012
- UniProtKB: Q66H30 (UniProtKB/Swiss-Prot),   A6JR80 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016028   ⟸   ENSRNOT00000016028
RefSeq Acc Id: ENSRNOP00000073007   ⟸   ENSRNOT00000087355
RefSeq Acc Id: XP_038939710   ⟸   XM_039083782
- Peptide Label: isoform X1
- UniProtKB: A0A8L2R6L5 (UniProtKB/TrEMBL),   A6JR80 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939713   ⟸   XM_039083785
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939712   ⟸   XM_039083784
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063123403   ⟸   XM_063267333
- Peptide Label: isoform X2
Protein Domains
Integrase catalytic

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66H30-F1-model_v2 AlphaFold Q66H30 1-518 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696898
Promoter ID:EPDNEW_R7421
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/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.09111,220,702 - 111,220,762EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307449 AgrOrtholog
BioCyc Gene G2FUF-26582 BioCyc
Ensembl Genes ENSRNOG00000011962 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055009507 UniProtKB/Swiss-Prot
  ENSRNOG00060001510 UniProtKB/Swiss-Prot
  ENSRNOG00065020029 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000016028 ENTREZGENE
  ENSRNOT00000016028.8 UniProtKB/Swiss-Prot
  ENSRNOT00000087355.2 UniProtKB/TrEMBL
  ENSRNOT00055016060 UniProtKB/Swiss-Prot
  ENSRNOT00060002265 UniProtKB/Swiss-Prot
  ENSRNOT00065033780 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.340.70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.420.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7132420 IMAGE-MGC_LOAD
InterPro Integrase_cat-core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Integrase_H2C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RNaseH-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RNaseH_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:316687 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95212 IMAGE-MGC_LOAD
NCBI Gene 316687 ENTREZGENE
PANTHER ENDONUCLEASE-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GYPSY RETROTRANSPOSON INTEGRASE-LIKE PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Integrase_H2C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gin1 PhenoGen
PROSITE INTEGRASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011962 RatGTEx
  ENSRNOG00055009507 RatGTEx
  ENSRNOG00060001510 RatGTEx
  ENSRNOG00065020029 RatGTEx
Superfamily-SCOP SSF53098 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2R6L5 ENTREZGENE, UniProtKB/TrEMBL
  A6JR80 ENTREZGENE, UniProtKB/TrEMBL
  GIN1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Gin1  gypsy retrotransposon integrase 1  RGD1307449  similar to RIKEN cDNA 4930429M06Rik  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1307449  similar to RIKEN cDNA 4930429M06Rik  RGD1307449_predicted  similar to RIKEN cDNA 4930429M06Rik (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1307449_predicted  similar to RIKEN cDNA 4930429M06Rik (predicted)  LOC316687_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC316687_predicted  similar to RIKEN cDNA 4930429M06Rik (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL