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    ABLIM3 actin binding LIM protein family member 3 [ Homo sapiens (human) ]

    Gene ID: 22885, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ABLIM3provided by HGNC
    Official Full Name
    actin binding LIM protein family member 3provided by HGNC
    Primary source
    HGNC:HGNC:29132
    See related
    Ensembl:ENSG00000173210 MIM:611305; AllianceGenome:HGNC:29132
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HMFN1661
    Summary
    This gene encodes a member of the actin-binding LIM (abLIM) family of proteins. These proteins are characterized by an N-terminal LIM domain and a C-terminal dematin-like domain. The encoded protein interacts with actin filaments and may be a component of adherens junctions in several cell types. A variant of this gene may be associated with pain sensitivity in male human patients. [provided by RefSeq, Sep 2016]
    Expression
    Broad expression in fat (RPKM 33.5), heart (RPKM 19.5) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ABLIM3 in Genome Data Viewer
    Location:
    5q32
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (149141493..149260542)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (149676400..149795360)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (148521056..148640105)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10809 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:148452563-148453762 Neighboring gene SH3TC2 divergent transcript Neighboring gene RN7SK pseudogene 145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148521477-148521978 Neighboring gene uncharacterized LOC124901102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148521979-148522478 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82052 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82053 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:148566792-148567991 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148651401-148651940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148651941-148652482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148652483-148653022 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:148668739-148669240 Neighboring gene actin filament associated protein 1 like 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148696780-148697334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:148697335-148697887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148701677-148702203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148702204-148702729 Neighboring gene uncharacterized LOC124901103 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:148724745-148725370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:148725371-148725994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:148726519-148727019 Neighboring gene GRPEL2 antisense RNA 1 Neighboring gene GrpE like 2, mitochondrial

    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. Integrative approach to pain genetics identifies pain sensitivity loci across diseases. Ruau D, et al. PLoS Comput Biol, 2012. PMID 22685391, Free PMC Article
    2. Actin binding LIM protein 3 (abLIM3). Krupp M, et al. Int J Mol Med, 2006 Jan. PMID 16328021
    3. hhLIM protein is involved in cardiac hypertrophy. Zheng B, et al. Biochim Biophys Acta, 2004 Sep 6. PMID 15337165
    4. abLIM3 is a novel component of adherens junctions with actin-binding activity. Matsuda M, et al. Eur J Cell Biol, 2010 Nov. PMID 20709423
    5. Two novel members of the ABLIM protein family, ABLIM-2 and -3, associate with STARS and directly bind F-actin. Barrientos T, et al. J Biol Chem, 2007 Mar 16. PMID 17194709

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lamellipodium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within lamellipodium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein targeting to mitochondrion HMP PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lamellipodium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in stress fiber IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    actin-binding LIM protein 3
    Names
    abLIM-3

    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_051566.1 RefSeqGene

      Range
      5047..124096
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001301015.3 → NP_001287944.1  actin-binding LIM protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001287944.1

      Status: REVIEWED

      Source sequence(s)
      AC012613, AC091940
      Consensus CDS
      CCDS4294.1
      UniProtKB/Swiss-Prot
      A8K121, O94929, Q19VH3, Q658S1, Q68CI5, Q9BV32
      Related
      ENSP00000425394.1, ENST00000506113.5
      Conserved Domains (6) summary
      smart00153
      Location:648 → 683
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 647
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    2. NM_001301018.3 → NP_001287947.1  actin-binding LIM protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001287947.1

      Status: REVIEWED

      Source sequence(s)
      AB020650, AC012613, AC091940, AK225769, DA669720, DQ413174
      Consensus CDS
      CCDS78069.1
      UniProtKB/TrEMBL
      A0A0C4DGA7
      Conserved Domains (6) summary
      smart00153
      Location:615 → 650
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 614
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    3. NM_001301028.3 → NP_001287957.1  actin-binding LIM protein 3 isoform 4

      See identical proteins and their annotated locations for NP_001287957.1

      Status: REVIEWED

      Source sequence(s)
      AC012613, AC091940
      Consensus CDS
      CCDS78071.1
      UniProtKB/Swiss-Prot
      O94929
      Related
      ENSP00000421183.1, ENST00000504238.5
      Conserved Domains (5) summary
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 535
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    4. NM_001345858.2 → NP_001332787.1  actin-binding LIM protein 3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC012613, AC091940, AL833021
      UniProtKB/Swiss-Prot
      O94929
      Conserved Domains (6) summary
      smart00153
      Location:599 → 634
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 598
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    5. NM_001345859.2 → NP_001332788.1  actin-binding LIM protein 3 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC012613, AC091940, AL833021
      Consensus CDS
      CCDS87335.1
      UniProtKB/Swiss-Prot
      O94929
      Related
      ENSP00000315841.7, ENST00000326685.11
      Conserved Domains (6) summary
      smart00153
      Location:553 → 588
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:273 → 552
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    6. NM_001345860.2 → NP_001332789.1  actin-binding LIM protein 3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC012613, AC091940, AL833021
      UniProtKB/Swiss-Prot
      O94929
      Conserved Domains (6) summary
      smart00153
      Location:537 → 572
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:273 → 536
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    7. NM_001345861.2 → NP_001332790.1  actin-binding LIM protein 3 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC012613, AC091940
      Consensus CDS
      CCDS87335.1
      UniProtKB/Swiss-Prot
      O94929
      Conserved Domains (6) summary
      smart00153
      Location:553 → 588
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:273 → 552
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    8. NM_001370417.1 → NP_001357346.1  actin-binding LIM protein 3 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC012613, AC091940
      Consensus CDS
      CCDS78069.1
      UniProtKB/TrEMBL
      A0A0C4DGA7
      Related
      ENSP00000420855.1, ENST00000508983.5
      Conserved Domains (6) summary
      smart00153
      Location:615 → 650
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 614
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    9. NM_001370418.1 → NP_001357347.1  actin-binding LIM protein 3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC012613, AC091940
      Conserved Domains (6) summary
      smart00153
      Location:537 → 572
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:273 → 536
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    10. NM_014945.5 → NP_055760.1  actin-binding LIM protein 3 isoform 1

      See identical proteins and their annotated locations for NP_055760.1

      Status: REVIEWED

      Source sequence(s)
      AC012613, AK225769, AK289736, BC001665, BP285049
      Consensus CDS
      CCDS4294.1
      UniProtKB/Swiss-Prot
      A8K121, O94929, Q19VH3, Q658S1, Q68CI5, Q9BV32
      Related
      ENSP00000310309.7, ENST00000309868.12
      Conserved Domains (6) summary
      smart00153
      Location:648 → 683
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 647
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      149141493..149260542
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005268394.3 → XP_005268451.1  actin-binding LIM protein 3 isoform X2

      See identical proteins and their annotated locations for XP_005268451.1

      Conserved Domains (6) summary
      smart00153
      Location:586 → 621
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:273 → 585
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    2. XM_011537609.4 → XP_011535911.1  actin-binding LIM protein 3 isoform X4

      Conserved Domains (5) summary
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 435
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    3. XM_024446006.2 → XP_024301774.1  actin-binding LIM protein 3 isoform X3

      Conserved Domains (5) summary
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 351
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    4. XM_024446004.2 → XP_024301772.1  actin-binding LIM protein 3 isoform X1

      Conserved Domains (6) summary
      smart00153
      Location:599 → 634
      VHP; Villin headpiece domain
      cd09327
      Location:23 → 74
      LIM1_abLIM; The first LIM domain of actin binding LIM (abLIM) proteins
      cd09328
      Location:79 → 134
      LIM2_abLIM; The second LIM domain on actin binding LIM (abLIM) proteins
      cd09329
      Location:151 → 202
      LIM3_abLIM; The third LIM domain of actin binding LIM (abLIM) proteins
      cd09330
      Location:210 → 265
      LIM4_abLIM; The fourth LIM domain of actin binding LIM (abLIM) proteins
      pfam16182
      Location:274 → 598
      AbLIM_anchor; Putative adherens-junction anchoring region of AbLIM

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      149676400..149795360
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352094.1 → XP_054208069.1  actin-binding LIM protein 3 isoform X2

    2. XM_054352096.1 → XP_054208071.1  actin-binding LIM protein 3 isoform X4

    3. XM_054352095.1 → XP_054208070.1  actin-binding LIM protein 3 isoform X3

    4. XM_054352093.1 → XP_054208068.1  actin-binding LIM protein 3 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001301027.2: Suppressed sequence

      Description
      NM_001301027.2: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O94929.3 GenPept UniProtKB/Swiss-Prot:O94929

    Gene LinkOut

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

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