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RIPOR3 RIPOR family member 3 [ Homo sapiens (human) ]

Gene ID: 140876, updated on 3-Apr-2024

Summary

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Official Symbol
RIPOR3provided by HGNC
Official Full Name
RIPOR family member 3provided by HGNC
Primary source
HGNC:HGNC:16168
See related
Ensembl:ENSG00000042062 AllianceGenome:HGNC:16168
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FAM65C; C20orf175; C20orf176
Expression
Broad expression in bone marrow (RPKM 7.7), kidney (RPKM 6.8) and 22 other tissues See more
Orthologs
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Genomic context

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See RIPOR3 in Genome Data Viewer
Location:
20q13.13
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (50586108..50691542, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (52355766..52462307, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (49202645..49308079, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase non-receptor type 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:49177610-49178809 Neighboring gene RNA, 7SL, cytoplasmic 672, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49202858-49203371 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49203372-49203884 Neighboring gene Sharpr-MPRA regulatory region 3633 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49218491-49218991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49227064-49227564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49233537-49234037 Neighboring gene microRNA 645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49241541-49242502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49245378-49245975 Neighboring gene microRNA 1302-5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49256745-49257440 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49261035-49261616 Neighboring gene ribosomal protein L36 pseudogene 2 Neighboring gene RIPOR3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49282430-49282930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49282931-49283431 Neighboring gene uncharacterized LOC105372659 Neighboring gene VISTA enhancer hs1860 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:49313764-49313925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49320243-49320744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49320745-49321244 Neighboring gene CRISPRi-validated cis-regulatory element chr20.2420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13023 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:49345068-49346267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13024 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13025 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:49353859-49354534 Neighboring gene par-6 family cell polarity regulator beta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49406827-49407512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18099 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13027 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49436893-49437394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18105 Neighboring gene breast carcinoma amplified sequence 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49450347-49450846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49453840-49454668 Neighboring gene TMSB4X pseudogene 6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Downregulated Expression of RIPOR3 Correlated with Immune Infiltrates Predicts Poor Prognosis in Oral Tongue Cancer. Zhang K, et al. Med Sci Monit, 2022 Mar 12. PMID 35277469, Free PMC Article
  2. A transcript finishing initiative for closing gaps in the human transcriptome. Sogayar MC, et al. Genome Res, 2004 Jul. PMID 15197164, Free PMC Article
  3. Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants. Wistow G, et al. Mol Vis, 2002 Jun 15. PMID 12107410
  4. The DNA sequence and comparative analysis of human chromosome 20. Deloukas P, et al. Nature, 2001 Dec 20-27. PMID 11780052
  5. Transcriptome analysis of human gastric cancer. Oh JH, et al. Mamm Genome, 2005 Dec. PMID 16341674

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Downregulated Expression of RIPOR3 Correlated with Immune Infiltrates Predicts Poor Prognosis in Oral Tongue Cancer.
    Title: Downregulated Expression of RIPOR3 Correlated with Immune Infiltrates Predicts Poor Prognosis in Oral Tongue Cancer.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ00360, FLJ32230

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
RIPOR family member 3
Names
family with sequence similarity 65 member C
protein FAM65C

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_034040.1 RefSeqGene

    Range
    4989..110423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001290268.2 → NP_001277197.1  RIPOR family member 3 isoform 2

    See identical proteins and their annotated locations for NP_001277197.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate upstream AUG compared to variant 1. The encoded protein (isoform 2) has a longer N-terminus compared to isoform 1.
    Source sequence(s)
    AI056877, AK295781, AK299337, AL353653, AV703941, BM846795, BX111440, CD558804, CF272670, DC400584
    Consensus CDS
    CCDS93056.1
    UniProtKB/TrEMBL
    A0A499FJE4, B7Z5S0
    Related
    ENSP00000332663.3, ENST00000327979.8
    Conserved Domains (1) summary
    pfam15903
    Location:23 → 367
    PL48; Filopodia upregulated, FAM65

  2. NM_080829.4 → NP_543019.2  RIPOR family member 3 isoform 1

    See identical proteins and their annotated locations for NP_543019.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the shorter protein (isoform 1).
    Source sequence(s)
    AI056877, AK056792, AL133230, AL732057, CA389799, CF272670, CN268262, DT932687
    Consensus CDS
    CCDS13431.2
    UniProtKB/Swiss-Prot
    Q5QPB6, Q96MK2, Q9NQQ2
    UniProtKB/TrEMBL
    B7Z5S0
    Related
    ENSP00000045083.2, ENST00000045083.6
    Conserved Domains (1) summary
    pfam15903
    Location:19 → 363
    PL48; Filopodia upregulated, FAM65

RNA

  1. NR_110890.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate first exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK295781, AK299337, AL353653, BQ446237, BX111440, CD558804, CF272670, DC365439, HY221639, HY285972

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    50586108..50691542 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006723713.5 → XP_006723776.1  RIPOR family member 3 isoform X2

    UniProtKB/TrEMBL
    B7Z5S0
    Conserved Domains (1) summary
    pfam15903
    Location:23 → 362
    PL48; Filopodia upregulated, FAM65

  2. XM_011528579.3 → XP_011526881.1  RIPOR family member 3 isoform X1

    See identical proteins and their annotated locations for XP_011526881.1

    UniProtKB/Swiss-Prot
    Q5QPB6, Q96MK2, Q9NQQ2
    UniProtKB/TrEMBL
    B7Z5S0
    Conserved Domains (1) summary
    pfam15903
    Location:19 → 363
    PL48; Filopodia upregulated, FAM65

  3. XM_047439913.1 → XP_047295869.1  RIPOR family member 3 isoform X1

    UniProtKB/Swiss-Prot
    Q5QPB6, Q96MK2, Q9NQQ2

  4. XM_047439912.1 → XP_047295868.1  RIPOR family member 3 isoform X1

    UniProtKB/Swiss-Prot
    Q5QPB6, Q96MK2, Q9NQQ2

  5. XM_017027681.1 → XP_016883170.1  RIPOR family member 3 isoform X3

    Conserved Domains (1) summary
    pfam15903
    Location:1 → 137
    PL48; Filopodia upregulated, FAM65

  6. XM_011528585.3 → XP_011526887.1  RIPOR family member 3 isoform X6

    Conserved Domains (2) summary
    PHA03089
    Location:433 → 474
    PHA03089; late transcription factor VLTF-4; Provisional
    pfam15903
    Location:1 → 30
    PL48; Filopodia upregulated, FAM65

  7. XM_047439914.1 → XP_047295870.1  RIPOR family member 3 isoform X4

  8. XM_011528584.4 → XP_011526886.1  RIPOR family member 3 isoform X5

    UniProtKB/TrEMBL
    B7Z3F0
    Conserved Domains (1) summary
    pfam15903
    Location:23 → 367
    PL48; Filopodia upregulated, FAM65

  9. XM_011528586.3 → XP_011526888.1  RIPOR family member 3 isoform X7

    UniProtKB/TrEMBL
    B7Z3F0
    Conserved Domains (1) summary
    pfam15903
    Location:23 → 367
    PL48; Filopodia upregulated, FAM65

RNA

  1. XR_936505.3 RNA Sequence

  2. XR_936506.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    52355766..52462307 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323036.1 → XP_054179011.1  RIPOR family member 3 isoform X8

    UniProtKB/TrEMBL
    A0A499FJE4

  2. XM_054323037.1 → XP_054179012.1  RIPOR family member 3 isoform X8

    UniProtKB/TrEMBL
    A0A499FJE4

  3. XM_054323041.1 → XP_054179016.1  RIPOR family member 3 isoform X2

  4. XM_054323038.1 → XP_054179013.1  RIPOR family member 3 isoform X1

    UniProtKB/Swiss-Prot
    Q5QPB6, Q96MK2, Q9NQQ2

  5. XM_054323040.1 → XP_054179015.1  RIPOR family member 3 isoform X1

    UniProtKB/Swiss-Prot
    Q5QPB6, Q96MK2, Q9NQQ2

  6. XM_054323039.1 → XP_054179014.1  RIPOR family member 3 isoform X1

    UniProtKB/Swiss-Prot
    Q5QPB6, Q96MK2, Q9NQQ2

  7. XM_054323042.1 → XP_054179017.1  RIPOR family member 3 isoform X3

  8. XM_054323045.1 → XP_054179020.1  RIPOR family member 3 isoform X6

  9. XM_054323043.1 → XP_054179018.1  RIPOR family member 3 isoform X4

  10. XM_054323044.1 → XP_054179019.1  RIPOR family member 3 isoform X5

  11. XM_054323046.1 → XP_054179021.1  RIPOR family member 3 isoform X7

RNA

  1. XR_008485235.1 RNA Sequence

  2. XR_008485236.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96MK2.4 GenPept UniProtKB/Swiss-Prot:Q96MK2

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