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Aliases for RINT1 Gene

Aliases for RINT1 Gene

  • RAD50 Interactor 1 2 3 4 5
  • RINT-1 3 4
  • RAD50-Interacting Protein 1 3
  • HsRINT-1 4

External Ids for RINT1 Gene

Previous GeneCards Identifiers for RINT1 Gene

  • GC07P104959
  • GC07P105172
  • GC07P099530

Summaries for RINT1 Gene

Entrez Gene Summary for RINT1 Gene

  • This gene encodes a protein first identified for its ability to interact with the RAD50 double strand break repair protein, with the resulting interaction implicated in the regulation of cell cycle progression and telomere length. The encoded protein may also play a role in trafficking of cellular cargo from the endosome to the trans-Golgi network. Mutations in this gene may be associated with breast cancer in human patients. [provided by RefSeq, Oct 2016]

GeneCards Summary for RINT1 Gene

RINT1 (RAD50 Interactor 1) is a Protein Coding gene. Diseases associated with RINT1 include Lynch Syndrome. Among its related pathways are Golgi-to-ER retrograde transport and Vesicle-mediated transport.

UniProtKB/Swiss-Prot for RINT1 Gene

  • Involved in regulation of membrane traffic between the Golgi and the endoplasmic reticulum (ER); the function is proposed to depend on its association in the NRZ complex which is believed to play a role in SNARE assembly at the ER. May play a role in cell cycle checkpoint control (PubMed:11096100). Essential for telomere length control (PubMed:16600870).

Gene Wiki entry for RINT1 Gene

Additional gene information for RINT1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RINT1 Gene

Genomics for RINT1 Gene

GeneHancer (GH) Regulatory Elements for RINT1 Gene

Promoters and enhancers for RINT1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J105531 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 674.2 +0.5 465 2.8 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 RINT1 PUS7 ATXN7L1 LOC100131785 KMT2E KMT2E-AS1 EIF4BP6 ENSG00000272604 GC07P105567
GH07J105005 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE dbSUPER 62.7 -519.8 -519781 12.7 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 KMT2E LINC01004 ATXN7L1 RINT1 EIF4BP6 ORC5 KMT2E-AS1 PUS7 YBX1P2 RPL36P12
GH07J104940 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 29.3 -588.4 -588438 6.5 FEZF1 DMAP1 YBX1 IRF4 SLC30A9 ZNF213 ZNF143 SP3 NFYC MEF2D ORC5 ATXN7L1 RINT1 LINC01004 KMT2E RNU6-1322P KMT2E-AS1 LOC101927902 SRPK2 GC07P104968
GH07J106281 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 25.3 +752.2 752154 4.9 CLOCK YBX1 DMAP1 IRF4 YY1 E2F8 ZNF143 SP3 GLIS1 NBN NAMPT GC07M106278 ENSG00000273320 ENSG00000272072 ATXN7L1 RINT1 HBP1 PUS7 RNU6-392P
GH07J106344 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 33.6 +814.0 814030 3.8 HDGF PKNOX1 ATF1 ARNT IRF4 BRCA1 TCF12 ZNF766 FOS ATF7 NAMPT RINT1 ENSG00000272072 HBP1 PUS7 ATXN7L1 CCDC71L LARP1BP2 ENSG00000267052
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RINT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RINT1 gene promoter:
  • deltaCREB
  • CREB
  • Pax-4a
  • AML1a
  • MyoD
  • HNF-4alpha2
  • HNF-4alpha1
  • HOXA9
  • HOXA9B

Genomic Locations for RINT1 Gene

Genomic Locations for RINT1 Gene
chr7:105,532,085-105,567,678
(GRCh38/hg38)
Size:
35,594 bases
Orientation:
Plus strand
chr7:105,172,532-105,208,124
(GRCh37/hg19)
Size:
35,593 bases
Orientation:
Plus strand

Genomic View for RINT1 Gene

Genes around RINT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RINT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RINT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RINT1 Gene

Proteins for RINT1 Gene

  • Protein details for RINT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6NUQ1-RINT1_HUMAN
    Recommended name:
    RAD50-interacting protein 1
    Protein Accession:
    Q6NUQ1
    Secondary Accessions:
    • Q75MG9
    • Q75MH0
    • Q96IW8
    • Q9H229
    • Q9HAD9

    Protein attributes for RINT1 Gene

    Size:
    792 amino acids
    Molecular mass:
    90632 Da
    Quaternary structure:
    • Component of the NRZ complex composed of NBAS, ZW10 and RINT1/TIP20L; NRZ associates with SNAREs STX18, USE1L, BNIP1/SEC20L and SEC22B (the assembly has been described as syntaxin 18 complex) (PubMed:15029241, PubMed:20462495, PubMed:19369418). Interacts directly with BNIP1/SEC20L and ZW10 (PubMed:15029241, PubMed:15272311). Interacts with UVRAG (PubMed:24056303). Interacts with RAD50 during late S and G2/M phases (PubMed:11096100). Interacts with RBL2, preferentially with the active, hypophosphorylated form (PubMed:16600870).
    Miscellaneous:
    • According to PubMed:11096100, a longer form, which may be due to the differential initiation of translation using a non-AUG codon, may exist. However, the existence of such form has not been clearly demonstrated.
    SequenceCaution:
    • Sequence=AAG42101.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAQ96849.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=AAQ96850.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAB13910.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for RINT1 Gene

Post-translational modifications for RINT1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RINT1 Gene

Domains & Families for RINT1 Gene

Gene Families for RINT1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RINT1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RINT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6NUQ1

UniProtKB/Swiss-Prot:

RINT1_HUMAN :
  • Belongs to the RINT1 family.
Family:
  • Belongs to the RINT1 family.
genes like me logo Genes that share domains with RINT1: view

Function for RINT1 Gene

Molecular function for RINT1 Gene

UniProtKB/Swiss-Prot Function:
Involved in regulation of membrane traffic between the Golgi and the endoplasmic reticulum (ER); the function is proposed to depend on its association in the NRZ complex which is believed to play a role in SNARE assembly at the ER. May play a role in cell cycle checkpoint control (PubMed:11096100). Essential for telomere length control (PubMed:16600870).

Gene Ontology (GO) - Molecular Function for RINT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11096100
genes like me logo Genes that share ontologies with RINT1: view
genes like me logo Genes that share phenotypes with RINT1: view

Animal Models for RINT1 Gene

MGI Knock Outs for RINT1:

Animal Model Products

miRNA for RINT1 Gene

miRTarBase miRNAs that target RINT1

Clone Products

  • Addgene plasmids for RINT1

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RINT1 Gene

Localization for RINT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RINT1 Gene

Cytoplasm. Endoplasmic reticulum membrane; Peripheral membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RINT1 gene
Compartment Confidence
endoplasmic reticulum 5
cytosol 5
golgi apparatus 3
nucleus 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RINT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IEA,IDA 15029241
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005829 cytosol TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with RINT1: view

Pathways & Interactions for RINT1 Gene

genes like me logo Genes that share pathways with RINT1: view

Gene Ontology (GO) - Biological Process for RINT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER TAS --
GO:0007049 cell cycle IEA --
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IEA --
GO:0048193 Golgi vesicle transport IEA --
genes like me logo Genes that share ontologies with RINT1: view

No data available for SIGNOR curated interactions for RINT1 Gene

Drugs & Compounds for RINT1 Gene

No Compound Related Data Available

Transcripts for RINT1 Gene

Unigene Clusters for RINT1 Gene

RAD50 interactor 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for RINT1

Alternative Splicing Database (ASD) splice patterns (SP) for RINT1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c · 11d ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b · 15c ^ 16a · 16b ^ 17a ·
SP1: - - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10: -
SP11: - - -
SP12: - - - -
SP13:

ExUns: 17b · 17c ^ 18a · 18b · 18c ^ 19 ^ 20
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for RINT1 Gene

GeneLoc Exon Structure for
RINT1
ECgene alternative splicing isoforms for
RINT1

Expression for RINT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RINT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RINT1 Gene

This gene is overexpressed in Bone (28.4) and Nasal epithelium (22.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RINT1 Gene



Protein tissue co-expression partners for RINT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RINT1 Gene:

RINT1

SOURCE GeneReport for Unigene cluster for RINT1 Gene:

Hs.531388

Evidence on tissue expression from TISSUES for RINT1 Gene

  • Nervous system(4.6)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with RINT1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RINT1 Gene

Orthologs for RINT1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RINT1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RINT1 34 33
  • 99.71 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RINT1 34 33
  • 91.41 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RINT1 34 33
  • 90.19 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RINT1 34
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rint1 16 34 33
  • 84.64 (n)
rat
(Rattus norvegicus)
Mammalia Rint1 33
  • 82.85 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RINT1 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves RINT1 34 33
  • 76.79 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RINT1 34
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rint1 33
  • 72.84 (n)
Str.9349 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.13145 33
zebrafish
(Danio rerio)
Actinopterygii rint1 34 33
  • 60.27 (n)
OneToOne
Dr.28007 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007482 33
  • 45.59 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8605 34 33
  • 43.17 (n)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU02270 33
  • 40.51 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 38 (a)
OneToOne
Species where no ortholog for RINT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RINT1 Gene

ENSEMBL:
Gene Tree for RINT1 (if available)
TreeFam:
Gene Tree for RINT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RINT1: view image

Paralogs for RINT1 Gene

No data available for Paralogs for RINT1 Gene

Variants for RINT1 Gene

Sequence variations from dbSNP and Humsavar for RINT1 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs374658950 likely-benign, Cowden syndrome 105,542,464(+) A/G 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs869312981 uncertain-significance, Cowden syndrome 105,555,224(+) TGTTGT/TGT coding_sequence_variant, intron_variant, splice_donor_variant
rs869312982 uncertain-significance, Cowden syndrome 105,551,683(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1060504806 likely-benign, not specified 105,550,443(+) A/G coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1060504807 likely-benign, not specified 105,532,865(+) G/A/C 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for RINT1 Gene

Variant ID Type Subtype PubMed ID
dgv6547n100 CNV gain 25217958
esv2759549 CNV gain 17122850
esv3614417 CNV gain 21293372
esv3614426 CNV gain 21293372
esv3614427 CNV gain 21293372
esv3614428 CNV loss 21293372
esv3891174 CNV gain 25118596
nsv1023564 CNV gain 25217958
nsv464668 CNV gain 19166990
nsv608069 CNV gain 21841781

Variation tolerance for RINT1 Gene

Residual Variation Intolerance Score: 28.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.58; 72.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RINT1 Gene

Human Gene Mutation Database (HGMD)
RINT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RINT1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RINT1 Gene

Disorders for RINT1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RINT1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
lynch syndrome
  • colorectal cancer, hereditary nonpolyposis, type 1
- elite association - COSMIC cancer census association via MalaCards
Search RINT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RINT1

genes like me logo Genes that share disorders with RINT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RINT1 Gene

Publications for RINT1 Gene

  1. Implication of ZW10 in membrane trafficking between the endoplasmic reticulum and Golgi. (PMID: 15029241) Hirose H … Tagaya M (The EMBO journal 2004) 2 3 4 22 58
  2. RINT-1, a novel Rad50-interacting protein, participates in radiation-induced G(2)/M checkpoint control. (PMID: 11096100) Xiao J … Lee WH (The Journal of biological chemistry 2001) 2 3 4 22 58
  3. Structural analysis of the RZZ complex reveals common ancestry with multisubunit vesicle tethering machinery. (PMID: 20462495) Civril F … Musacchio A (Structure (London, England : 1993) 2010) 3 4 22 58
  4. The Rb-related p130 protein controls telomere lengthening through an interaction with a Rad50-interacting protein, RINT-1. (PMID: 16600870) Kong LJ … Nevins JR (Molecular cell 2006) 3 4 22 58
  5. PtdIns(3)P-bound UVRAG coordinates Golgi-ER retrograde and Atg9 transport by differential interactions with the ER tether and the beclin 1 complex. (PMID: 24056303) He S … Liang C (Nature cell biology 2013) 3 4 58

Products for RINT1 Gene

Sources for RINT1 Gene

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