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

Gene ID: 22885, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (149141493..149260542)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (149676400..149795360)
105.20220307 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: 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. 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)

Genotypes

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_2023_10

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

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