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    CDR2L cerebellar degeneration related protein 2 like [ Homo sapiens (human) ]

    Gene ID: 30850, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CDR2Lprovided by HGNC
    Official Full Name
    cerebellar degeneration related protein 2 likeprovided by HGNC
    Primary source
    HGNC:HGNC:29999
    See related
    Ensembl:ENSG00000109089 AllianceGenome:HGNC:29999
    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
    HUMPPA
    Summary
    Enables identical protein binding activity. Predicted to be involved in Golgi to secretory granule transport and vesicle transport along microtubule. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in duodenum (RPKM 11.0), stomach (RPKM 7.1) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CDR2L in Genome Data Viewer
    Location:
    17q25.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (74987632..75005800)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (75879422..75897596)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (72983727..73001895)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene HID1 domain containing Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8947 Neighboring gene HID1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:72978097-72979046 Neighboring gene uncharacterized LOC124904058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:72983565-72984066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:72989567-72990068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:72990069-72990568 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:73008409-73009092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:73009093-73009775 Neighboring gene mitochondrial ribosomal protein L58 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73015923-73017122 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73021286-73021443 Neighboring gene RNA, U6 small nuclear 362, pseudogene

    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. CDR2L Antibodies: A New Player in Paraneoplastic Cerebellar Degeneration. Eichler TW, et al. PLoS One, 2013. PMID 23823982, Free PMC Article
    2. Paraneoplastic Cerebellar Degeneration: The Importance of Including CDR2L as a Diagnostic Marker. Herdlevær I, et al. Neurol Neuroimmunol Neuroinflamm, 2021 Mar. PMID 33531379, Free PMC Article
    3. CDR2L Is the Major Yo Antibody Target in Paraneoplastic Cerebellar Degeneration. Kråkenes T, et al. Ann Neurol, 2019 Aug. PMID 31148214
    4. A cerebellar degeneration-related protein 2-like cell-based assay for anti-Yo detection in patients with paraneoplastic cerebellar degeneration. Erikstad KI, et al. Eur J Neurol, 2023 Jun. PMID 36912432
    5. Genetic alterations and tumor immune attack in Yo paraneoplastic cerebellar degeneration. Small M, et al. Acta Neuropathol, 2018 Apr. PMID 29299667

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A cerebellar degeneration-related protein 2-like cell-based assay for anti-Yo detection in patients with paraneoplastic cerebellar degeneration.
      Title: A cerebellar degeneration-related protein 2-like cell-based assay for anti-Yo detection in patients with paraneoplastic cerebellar degeneration.
    2. Paraneoplastic Cerebellar Degeneration: The Importance of Including CDR2L as a Diagnostic Marker.
      Title: Paraneoplastic Cerebellar Degeneration: The Importance of Including CDR2L as a Diagnostic Marker.
    3. Paraneoplastic cerebellar degenerations with anti-Yo antibodies (Yo-PCD) tumors differed from the 116 control tumors by more abundant T and B cells infiltration occasionally organized in tertiary lymphoid structures harboring CDR2L protein deposits. 65% of Yo-PCD tumors cohort presented at least one somatic mutation in CDR2 and CDR2L with a predominance of missense mutations.
      Title: Genetic alterations and tumor immune attack in Yo paraneoplastic cerebellar degeneration.
    4. Both cerebellar degeneration related protein 2 (CDR2) and cerebellar degeneration-related antigen CDR2L (CDR2L) are more widely expressed than previously thought, both in normal and cancerous tissues.
      Title: Cerebellar degeneration-related proteins 2 and 2-like are present in ovarian cancer in patients with and without Yo antibodies.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to secretory granule transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle transport along microtubule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cerebellar degeneration-related protein 2-like
    Names
    paraneoplastic 62 kDa antigen
    paraneoplastic antigen

    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_014603.3 → NP_055418.2  cerebellar degeneration-related protein 2-like

      See identical proteins and their annotated locations for NP_055418.2

      Status: VALIDATED

      Source sequence(s)
      AC087651, AW239343, BC013105, BC047534
      Consensus CDS
      CCDS11710.2
      UniProtKB/Swiss-Prot
      B4DFA7, Q15175, Q86X02
      Related
      ENSP00000336587.5, ENST00000337231.5
      Conserved Domains (1) summary
      COG1196
      Location:2 → 241
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      74987632..75005800
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006721852.3 → XP_006721915.1  cerebellar degeneration-related protein 2-like isoform X1

      Conserved Domains (1) summary
      TIGR02168
      Location:23 → 225
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      75879422..75897596
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315894.1 → XP_054171869.1  cerebellar degeneration-related protein 2-like isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86X02.2 GenPept UniProtKB/Swiss-Prot:Q86X02

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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