Human Gene GIN1 (uc003koa.1)
  Description: Homo sapiens gypsy retrotransposon integrase 1 (GIN1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:102,421,704-102,455,842 Size: 34,139 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr5:102,423,602-102,444,411 Size: 20,810 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:102,421,704-102,455,842)mRNA (may differ from genome)Protein (522 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GIN1_HUMAN
DESCRIPTION: RecName: Full=Gypsy retrotransposon integrase-like protein 1; Short=GIN-1; AltName: Full=Ty3/Gypsy integrase 1; AltName: Full=Zinc finger H2C2 domain-containing protein;
TISSUE SPECIFICITY: Widely expressed. Also found in tumors originating from parathyroid gland, colon, stomach, bladder, uterus and prostate.
SIMILARITY: Contains 1 integrase catalytic domain.
SEQUENCE CAUTION: Sequence=BAA90963.1; Type=Frameshift; Positions=375; Sequence=CAH10511.1; Type=Miscellaneous discrepancy; Note=Wrong choice of CDS;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GIN1
CDC HuGE Published Literature: GIN1

-  MalaCards Disease Associations
  MalaCards Gene Search: GIN1
Diseases sorted by gene-association score: parametritis (3), osmotic diarrhea (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.37 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 86.25 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.6082-0.251 Picture PostScript Text
3' UTR -479.211898-0.252 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001584 - Integrase_cat-core
IPR012337 - RNaseH-like_dom
IPR015416 - Znf_H2C2_histone_UAS-bd

SCOP Domains:
53098 - Ribonuclease H-like

ModBase Predicted Comparative 3D Structure on Q9NXP7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding

Biological Process:
GO:0015074 DNA integration


-  Descriptions from all associated GenBank mRNAs
  CR627424 - Homo sapiens mRNA; cDNA DKFZp781I0575 (from clone DKFZp781I0575).
BC151135 - Homo sapiens gypsy retrotransposon integrase 1, mRNA (cDNA clone MGC:184047 IMAGE:9057035), complete cds.
BC157835 - Homo sapiens gypsy retrotransposon integrase 1, mRNA (cDNA clone MGC:189730 IMAGE:9057054), complete cds.
JD081229 - Sequence 62253 from Patent EP1572962.
JD229934 - Sequence 210958 from Patent EP1572962.
JD243557 - Sequence 224581 from Patent EP1572962.
JD269380 - Sequence 250404 from Patent EP1572962.
JD349510 - Sequence 330534 from Patent EP1572962.
JD441419 - Sequence 422443 from Patent EP1572962.
JD256343 - Sequence 237367 from Patent EP1572962.
JD441420 - Sequence 422444 from Patent EP1572962.
JD441421 - Sequence 422445 from Patent EP1572962.
JD564421 - Sequence 545445 from Patent EP1572962.
AK295796 - Homo sapiens cDNA FLJ61279 complete cds.
BC015325 - Homo sapiens gypsy retrotransposon integrase 1, mRNA (cDNA clone IMAGE:4414731), complete cds.
AK225572 - Homo sapiens mRNA for hypothetical protein LOC54826 variant, clone: LNF01107.
AK000132 - Homo sapiens cDNA FLJ20125 fis, clone COL06152.
JD528575 - Sequence 509599 from Patent EP1572962.
JD515830 - Sequence 496854 from Patent EP1572962.
JD431423 - Sequence 412447 from Patent EP1572962.
JF432633 - Synthetic construct Homo sapiens clone IMAGE:100073870 gypsy retrotransposon integrase 1 (GIN1) gene, encodes complete protein.
KJ902697 - Synthetic construct Homo sapiens clone ccsbBroadEn_12091 GIN1 gene, encodes complete protein.
JD171537 - Sequence 152561 from Patent EP1572962.
JD037950 - Sequence 18974 from Patent EP1572962.
JD273190 - Sequence 254214 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RXF7, B4DIV4, GIN1_HUMAN, NM_017676, NP_060146, Q6AI03, Q96BR2, Q9NXP7, TGIN1, ZH2C2
UCSC ID: uc003koa.1
RefSeq Accession: NM_017676
Protein: Q9NXP7 (aka GIN1_HUMAN)
CCDS: CCDS43349.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017676.2
exon count: 8CDS single in 3' UTR: no RNA size: 3549
ORF size: 1569CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3338.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.