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

    Gene ID: 140876, updated on 10-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (50586108..50691542, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (52355766..52462307, complement)
    RS_2024_09 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 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_2024_08

    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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