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    LIMS2 LIM zinc finger domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 55679, updated on 3-Dec-2024

    Summary

    Official Symbol
    LIMS2provided by HGNC
    Official Full Name
    LIM zinc finger domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:16084
    See related
    Ensembl:ENSG00000072163 MIM:607908; AllianceGenome:HGNC:16084
    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
    LGMD2W; PINCH2; MDRCMTT; PINCH-2
    Summary
    This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each domain forming two zinc fingers, which permit interactions which regulate cell shape and migration. A pseudogene of this gene is located on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
    Expression
    Broad expression in endometrium (RPKM 24.9), fat (RPKM 20.9) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LIMS2 in Genome Data Viewer
    Location:
    2q14.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (127638426..127681786, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (128073680..128117027, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (128396001..128439360, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373609 Neighboring gene myosin VIIB Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:128335179-128335732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16497 Neighboring gene uncharacterized LOC101927834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:128393428-128394374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:128394375-128395321 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:128395322-128396268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:128396269-128397214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:128406535-128407262 Neighboring gene Sharpr-MPRA regulatory region 7437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:128407989-128408715 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:128408716-128409441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:128416288-128416788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:128419363-128420360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:128420398-128420938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:128420939-128421478 Neighboring gene G protein-coupled receptor 17 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:128457593-128458792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11936 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:128478937-128480136 Neighboring gene SFT2 domain containing 3 Neighboring gene WD repeat domain 33 Neighboring gene MPRA-validated peak3854 silencer Neighboring gene MPRA-validated peak3855 silencer Neighboring gene MPRA-validated peak3856 silencer Neighboring gene MPRA-validated peak3857 silencer Neighboring gene RNY4 pseudogene 7

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Autosomal recessive limb-girdle muscular dystrophy type 2W
    MedGen: C4225192 OMIM: 616827 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10044

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell-cell junction organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cholangiocyte proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in integrin-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cholangiocyte proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of hepatocyte proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of integrin-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of substrate adhesion-dependent cell spreading IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in focal adhesion HDA PubMed 
    is_active_in focal adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    LIM and senescent cell antigen-like-containing domain protein 2
    Names
    ILK-binding protein
    LIM and senescent cell antigen-like domains 2
    LIM-type zinc finger domains 2
    particularly interesting new Cys-His protein 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_042235.1 RefSeqGene

      Range
      11257..48361
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136037.4NP_001129509.2  LIM and senescent cell antigen-like-containing domain protein 2 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This transcript represents variant 1 and encodes isoform 1.
      Source sequence(s)
      AC010976, AC074114, AK022470, AK055363, BC065816, DC356496, DR006887
      Consensus CDS
      CCDS54396.1
      UniProtKB/TrEMBL
      B3KNZ3
      Related
      ENSP00000443794.2, ENST00000545738.6
      Conserved Domains (5) summary
      cd09331
      Location:3795
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:98149
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:162212
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:218271
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:279332
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    2. NM_001161403.3NP_001154875.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001154875.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC010976, AC074114, BC065816, DR006887
      Consensus CDS
      CCDS54395.1
      UniProtKB/Swiss-Prot
      A6NLH0, B4DMV1, F5H6E6, Q7Z4I2, Q7Z4I6, Q7Z4I7, Q7Z4I8, Q8NFE7, Q9HA13
      UniProtKB/TrEMBL
      B3KNZ3
      Related
      ENSP00000347240.4, ENST00000355119.9
      Conserved Domains (5) summary
      cd09331
      Location:1573
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:76127
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:140190
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:196249
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:257310
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    3. NM_001161404.2NP_001154876.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform 5

      See identical proteins and their annotated locations for NP_001154876.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
      Source sequence(s)
      AC010976, AF527766, DA890151
      Consensus CDS
      CCDS54394.1
      UniProtKB/TrEMBL
      B3KNZ3
      Related
      ENSP00000387002.1, ENST00000410011.5
      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    4. NM_001256542.2NP_001243471.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform 4

      See identical proteins and their annotated locations for NP_001243471.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AF527770, BX458594, DA848179
      Consensus CDS
      CCDS58725.1
      UniProtKB/TrEMBL
      Q7Z4I3
      Related
      ENSP00000386570.1, ENST00000410038.5
      Conserved Domains (3) summary
      cd09334
      Location:4497
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:105158
      LIM5_PINCH; The fifth LIM domain of protein PINCH
      cl02475
      Location:238
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
    5. NM_017980.5NP_060450.2  LIM and senescent cell antigen-like-containing domain protein 2 isoform 2

      See identical proteins and their annotated locations for NP_060450.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is longer than isoform 1.
      Source sequence(s)
      AC074114, AF527764, AF527765, BP221000
      Consensus CDS
      CCDS2147.1
      UniProtKB/TrEMBL
      B3KNZ3
      Related
      ENSP00000326888.5, ENST00000324938.9
      Conserved Domains (5) summary
      cd09331
      Location:3997
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:100151
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:164214
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:220273
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:281334
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    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
      127638426..127681786 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006712627.5XP_006712690.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X9

      UniProtKB/TrEMBL
      Q7Z4I3
      Conserved Domains (3) summary
      cd09333
      Location:2474
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:80133
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:141194
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    2. XM_005263710.3XP_005263767.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X6

      UniProtKB/TrEMBL
      Q7Z4I5
      Conserved Domains (4) summary
      cd09332
      Location:758
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:71121
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:127180
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:188241
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    3. XM_047444970.1XP_047300926.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X4

    4. XM_024452983.2XP_024308751.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X2

      UniProtKB/TrEMBL
      B3KNZ3
      Related
      ENSP00000386637.2, ENST00000409808.6
      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    5. XM_011511453.2XP_011509755.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X3

      Conserved Domains (4) summary
      cd09331
      Location:3997
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:100151
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09335
      Location:240293
      LIM5_PINCH; The fifth LIM domain of protein PINCH
      cl02475
      Location:164205
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
    6. XM_047444963.1XP_047300919.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X1

      UniProtKB/TrEMBL
      B3KNZ3
    7. XM_024452986.2XP_024308754.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X11

      UniProtKB/TrEMBL
      Q7Z4I3
      Related
      ENSP00000386252.1, ENST00000409286.5
      Conserved Domains (3) summary
      cd09334
      Location:4497
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:105158
      LIM5_PINCH; The fifth LIM domain of protein PINCH
      cl02475
      Location:238
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
    8. XM_047444976.1XP_047300932.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X11

      UniProtKB/TrEMBL
      Q7Z4I3
    9. XM_047444975.1XP_047300931.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X11

      UniProtKB/TrEMBL
      Q7Z4I3
    10. XM_024452985.2XP_024308753.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X11

      UniProtKB/TrEMBL
      Q7Z4I3
      Conserved Domains (3) summary
      cd09334
      Location:4497
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:105158
      LIM5_PINCH; The fifth LIM domain of protein PINCH
      cl02475
      Location:238
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
    11. XM_047444972.1XP_047300928.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X7

      UniProtKB/TrEMBL
      Q7Z4I4
    12. XM_017004469.2XP_016859958.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X8

    13. XM_047444971.1XP_047300927.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X5

    14. XM_006712628.4XP_006712691.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X10

      Conserved Domains (2) summary
      cd09331
      Location:3997
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:100143
      LIM2_PINCH; The second LIM domain of protein PINCH

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      128073680..128117027 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342902.1XP_054198877.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X9

      UniProtKB/TrEMBL
      Q7Z4I3
    2. XM_054342899.1XP_054198874.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X6

      UniProtKB/TrEMBL
      Q7Z4I5
    3. XM_054342897.1XP_054198872.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X4

    4. XM_054342895.1XP_054198870.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X2

      UniProtKB/TrEMBL
      B3KNZ3
    5. XM_054342896.1XP_054198871.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X3

    6. XM_054342894.1XP_054198869.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X1

      UniProtKB/TrEMBL
      B3KNZ3
    7. XM_054342905.1XP_054198880.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X11

      UniProtKB/TrEMBL
      Q7Z4I3
    8. XM_054342904.1XP_054198879.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X11

      UniProtKB/TrEMBL
      Q7Z4I3
    9. XM_054342900.1XP_054198875.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X7

      UniProtKB/TrEMBL
      Q7Z4I4
    10. XM_054342901.1XP_054198876.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X8

    11. XM_054342898.1XP_054198873.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X5

    12. XM_054342903.1XP_054198878.1  LIM and senescent cell antigen-like-containing domain protein 2 isoform X10