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    RGPD6 RANBP2 like and GRIP domain containing 6 [ Homo sapiens (human) ]

    Gene ID: 729540, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RGPD6provided by HGNC
    Official Full Name
    RANBP2 like and GRIP domain containing 6provided by HGNC
    Primary source
    HGNC:HGNC:32419
    See related
    Ensembl:ENSG00000183054 MIM:612709; AllianceGenome:HGNC:32419
    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
    RGP6; RGPD7; RanBP2L1; RanBP2L2
    Summary
    Predicted to be involved in intracellular transport. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in testis (RPKM 24.0), brain (RPKM 8.3) and 25 other tissues See more
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    Genomic context

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    See RGPD6 in Genome Data Viewer
    Location:
    2q13
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (110513802..110611056, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (110936277..111033955, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (111271379..111368633, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene LIM zinc finger domain containing 4 Neighboring gene uncharacterized LOC105373552 Neighboring gene uncharacterized LOC102724875 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:111339275-111339775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:111367745-111368317 Neighboring gene uncharacterized LOC105373553 Neighboring gene ribosomal protein L22 pseudogene 12

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. Cantin GT, et al. J Proteome Res, 2008 Mar. PMID 18220336
    2. Identification of a novel Ran binding protein 2 related gene (RANBP2L1) and detection of a gene cluster on human chromosome 2q11-q12. Nothwang HG, et al. Genomics, 1998 Feb 1. PMID 9480752
    3. Complex genomic rearrangements lead to novel primate gene function. Ciccarelli FD, et al. Genome Res, 2005 Mar. PMID 15710750, Free PMC Article
    4. A quantitative atlas of mitotic phosphorylation. Dephoure N, et al. Proc Natl Acad Sci U S A, 2008 Aug 5. PMID 18669648, Free PMC Article
    5. Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Leparc GG, et al. Nucleic Acids Res, 2007. PMID 17452356, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC190070

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in NLS-bearing protein import into nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of nuclear pore IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RANBP2-like and GRIP domain-containing protein 5/6
    Names
    RANBP2-like and GRIP domain-containing protein 7
    ran-binding protein 2-like 1/2
    ranBP2-like 1/2

    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.

    mRNA and Protein(s)

    1. NM_001037866.2 → NP_001032955.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 2

      See identical proteins and their annotated locations for NP_001032955.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice pattern in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a substantially shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC108938, AC226101
      Consensus CDS
      CCDS42729.1
      Related
      ENSP00000330023.5, ENST00000330331.9
      Conserved Domains (3) summary
      sd00006
      Location:59 → 89
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:60 → 92
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:59 → 126
      TPR_11; TPR repeat

    2. NM_001123363.4 → NP_001116835.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 1

      See identical proteins and their annotated locations for NP_001116835.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC108938, AC226101
      Consensus CDS
      CCDS46388.1
      UniProtKB/Swiss-Prot
      Q53QN2, Q53T03, Q59GM7, Q99666, Q9H0B2
      UniProtKB/TrEMBL
      A0A8Q3SIN4, V9HWE4
      Related
      ENSP00000330842.3, ENST00000329516.8
      Conserved Domains (8) summary
      COG5171
      Location:975 → 1167
      YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
      cd13177
      Location:1051 → 1167
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1348 → 1464
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      sd00006
      Location:59 → 89
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:60 → 92
      TPR_1; Tetratricopeptide repeat
      pfam01465
      Location:1707 → 1749
      GRIP; GRIP domain
      pfam13414
      Location:59 → 126
      TPR_11; TPR repeat
      pfam16704
      Location:1641 → 1705
      Rab_bind; Rab binding domain

    3. NM_001384362.1 → NP_001371291.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      UniProtKB/TrEMBL
      J3KQ37
      Conserved Domains (4) summary
      cd13177
      Location:766 → 882
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1063 → 1179
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      pfam16704
      Location:1356 → 1420
      Rab_bind; Rab binding domain
      pfam01465
      Location:1422 → 1464
      GRIP; GRIP domain

    4. NM_001384363.1 → NP_001371292.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      Consensus CDS
      CCDS92839.1
      UniProtKB/TrEMBL
      A0A8Q3SII4, A0A8Q3SIN4
      Related
      ENSP00000512635.1, ENST00000696448.1
      Conserved Domains (7) summary
      COG0457
      Location:13 → 109
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      cd13177
      Location:1034 → 1150
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1331 → 1447
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      sd00006
      Location:42 → 72
      TPR; TPR repeat [structural motif]
      pfam16704
      Location:1624 → 1688
      Rab_bind; Rab binding domain
      pfam00515
      Location:43 → 75
      TPR_1; Tetratricopeptide repeat
      pfam01465
      Location:1690 → 1732
      GRIP; GRIP domain

    5. NM_001384364.1 → NP_001371293.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      UniProtKB/TrEMBL
      A0A8Q3SIN4
      Conserved Domains (7) summary
      COG0457
      Location:4 → 100
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      cd13177
      Location:1025 → 1141
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1322 → 1438
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      sd00006
      Location:33 → 63
      TPR; TPR repeat [structural motif]
      pfam16704
      Location:1615 → 1679
      Rab_bind; Rab binding domain
      pfam00515
      Location:34 → 66
      TPR_1; Tetratricopeptide repeat
      pfam01465
      Location:1681 → 1723
      GRIP; GRIP domain

    6. NM_001386141.1 → NP_001373070.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      UniProtKB/TrEMBL
      J3KQ37
      Conserved Domains (4) summary
      cd13177
      Location:766 → 882
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1063 → 1179
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      pfam16704
      Location:1356 → 1420
      Rab_bind; Rab binding domain
      pfam01465
      Location:1422 → 1464
      GRIP; GRIP domain

    7. NM_001386145.1 → NP_001373074.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      UniProtKB/TrEMBL
      A0A8Q3SIN4
      Conserved Domains (7) summary
      COG0457
      Location:29 → 125
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      cd13177
      Location:1050 → 1166
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1347 → 1463
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      sd00006
      Location:58 → 88
      TPR; TPR repeat [structural motif]
      pfam16704
      Location:1640 → 1704
      Rab_bind; Rab binding domain
      pfam00515
      Location:59 → 91
      TPR_1; Tetratricopeptide repeat
      pfam01465
      Location:1706 → 1748
      GRIP; GRIP domain

    8. NM_001386155.1 → NP_001373084.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      UniProtKB/TrEMBL
      J3KQ37
      Conserved Domains (4) summary
      cd13177
      Location:766 → 882
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1063 → 1179
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      pfam16704
      Location:1356 → 1420
      Rab_bind; Rab binding domain
      pfam01465
      Location:1422 → 1464
      GRIP; GRIP domain

    9. NM_001386159.1 → NP_001373088.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      UniProtKB/TrEMBL
      J3KQ37
      Conserved Domains (4) summary
      cd13177
      Location:766 → 882
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1063 → 1179
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      pfam16704
      Location:1356 → 1420
      Rab_bind; Rab binding domain
      pfam01465
      Location:1422 → 1464
      GRIP; GRIP domain

    10. NM_001386163.1 → NP_001373092.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      UniProtKB/TrEMBL
      B4DTT2
      Conserved Domains (4) summary
      cd13177
      Location:396 → 512
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:693 → 809
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      pfam16704
      Location:986 → 1050
      Rab_bind; Rab binding domain
      pfam01465
      Location:1052 → 1094
      GRIP; GRIP domain

    11. NM_001387273.1 → NP_001374202.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC108938, AC226101
      UniProtKB/TrEMBL
      J3KQ37
      Conserved Domains (4) summary
      cd13177
      Location:766 → 882
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1063 → 1179
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      pfam16704
      Location:1356 → 1420
      Rab_bind; Rab binding domain
      pfam01465
      Location:1422 → 1464
      GRIP; GRIP domain

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      110513802..110611056 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445731.1 → XP_047301687.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X2

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    2. XM_047445732.1 → XP_047301688.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X3

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    3. XM_017004839.2 → XP_016860328.2  RANBP2-like and GRIP domain-containing protein 5/6 isoform X1

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    4. XM_047445733.1 → XP_047301689.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X8

      UniProtKB/TrEMBL
      J3KQ37

    5. XM_017004841.2 → XP_016860330.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X4

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    6. XM_011511770.3 → XP_011510072.2  RANBP2-like and GRIP domain-containing protein 5/6 isoform X7

      UniProtKB/TrEMBL
      A0A8Q3SII5, A0A8Q3SIN4
      Related
      ENSP00000512636.1, ENST00000696449.1

    7. XM_011511769.3 → XP_011510071.2  RANBP2-like and GRIP domain-containing protein 5/6 isoform X5

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    8. XM_017004843.2 → XP_016860332.2  RANBP2-like and GRIP domain-containing protein 5/6 isoform X6

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      110936277..111033955 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343727.1 → XP_054199702.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X1

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    2. XM_054343732.1 → XP_054199707.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X8

      UniProtKB/TrEMBL
      J3KQ37

    3. XM_054343728.1 → XP_054199703.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X4

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    4. XM_054343731.1 → XP_054199706.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X7

      UniProtKB/TrEMBL
      A0A8Q3SII5, A0A8Q3SIN4

    5. XM_054343729.1 → XP_054199704.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X5

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    6. XM_054343730.1 → XP_054199705.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X6

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_169873.1: Suppressed sequence

      Description
      NR_169873.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99666.3 GenPept UniProtKB/Swiss-Prot:Q99666

    Gene LinkOut

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