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PHLDB2 pleckstrin homology like domain family B member 2 [ Homo sapiens (human) ]

Gene ID: 90102, updated on 19-Sep-2024

Summary

Official Symbol
PHLDB2provided by HGNC
Official Full Name
pleckstrin homology like domain family B member 2provided by HGNC
Primary source
HGNC:HGNC:29573
See related
Ensembl:ENSG00000144824 MIM:610298; AllianceGenome:HGNC:29573
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
LL5b; LL5beta
Summary
Enables cadherin binding activity. Involved in several processes, including negative regulation of focal adhesion assembly; regulation of cytoskeleton organization; and regulation of embryonic development. Located in several cellular components, including basal cortex; cell leading edge; and intermediate filament cytoskeleton. Colocalizes with focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in placenta (RPKM 18.1), kidney (RPKM 15.7) and 24 other tissues See more
Orthologs
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Genomic context

See PHLDB2 in Genome Data Viewer
Location:
3q13.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (111732496..111976517)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (114453343..114697610)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (111451343..111695364)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CD96 molecule Neighboring gene NT5C3A pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20225 Neighboring gene PLCXD2 antisense RNA 1 Neighboring gene phosphatidylinositol specific phospholipase C X domain containing 2 Neighboring gene Sharpr-MPRA regulatory region 10775 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:111453476-111454675 Neighboring gene uncharacterized LOC107984087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111511689-111512190 Neighboring gene uncharacterized LOC105374040 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111577934-111578520 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111578521-111579105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20226 Neighboring gene uncharacterized LOC124906336 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:111637713-111638912 Neighboring gene Sharpr-MPRA regulatory region 1117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111697515-111698074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:111704853-111705354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:111705355-111705854 Neighboring gene NANOG hESC enhancer GRCh37_chr3:111719684-111720311 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:111720792-111721991 Neighboring gene abhydrolase domain containing 10, depalmitoylase Neighboring gene transgelin 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: PLCXD2

Clone Names

  • FLJ21791, DKFZp434G227, DKFZp313O2433, DKFZp686J05113

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cadherin binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in cell migration IEA
Inferred from Electronic Annotation
more info
 
involved_in establishment of cell polarity IEA
Inferred from Electronic Annotation
more info
 
involved_in establishment of protein localization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in microtubule cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of focal adhesion assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of stress fiber assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of wound healing, spreading of epidermal cells IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of basement membrane assembly involved in embryonic body morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of basement membrane assembly involved in embryonic body morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of epithelial to mesenchymal transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of gastrulation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of microtubule cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of microtubule cytoskeleton organization IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
is_active_in basal cortex IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in basal cortex IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell cortex IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell leading edge IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
colocalizes_with focal adhesion IDA
Inferred from Direct Assay
more info
PubMed 
located_in intermediate filament cytoskeleton IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
located_in podosome IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
pleckstrin homology-like domain family B member 2
Names
LL5 beta
protein LL5-beta

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_001134437.2NP_001127909.1  pleckstrin homology-like domain family B member 2 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has a longer N-terminus and lacks an alternate internal segment compared to isoform a.
    Source sequence(s)
    AC060225, AF506820, AW264132, CA310697, CR749654, DA447763
    Consensus CDS
    CCDS46885.1
    UniProtKB/TrEMBL
    E9PFQ4
    Related
    ENSP00000377500.3, ENST00000393923.7
    Conserved Domains (4) summary
    cd14673
    Location:11261230
    PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
    pfam00169
    Location:11291225
    PH; PH domain
    cl02488
    Location:610774
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
    cl19107
    Location:10201089
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
  2. NM_001134438.2NP_001127910.1  pleckstrin homology-like domain family B member 2 isoform a

    See identical proteins and their annotated locations for NP_001127910.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC060225, AK315050, AW264132, DA438817
    Consensus CDS
    CCDS46886.1
    UniProtKB/Swiss-Prot
    A5PKZ3, Q59EA8, Q68CY3, Q6NT98, Q86SQ0, Q8N8U8, Q8NAB1, Q8NCU5
    UniProtKB/TrEMBL
    E9PFQ4
    Related
    ENSP00000405405.2, ENST00000431670.7
    Conserved Domains (5) summary
    cd14673
    Location:11421246
    PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
    pfam00169
    Location:11451241
    PH; PH domain
    pfam06008
    Location:524779
    Laminin_I; Laminin Domain I
    cl02488
    Location:583790
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
    cl19107
    Location:10361095
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
  3. NM_001134439.2NP_001127911.1  pleckstrin homology-like domain family B member 2 isoform a

    See identical proteins and their annotated locations for NP_001127911.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AB209903, AC060225, AW264132, DA272187
    Consensus CDS
    CCDS46886.1
    UniProtKB/Swiss-Prot
    A5PKZ3, Q59EA8, Q68CY3, Q6NT98, Q86SQ0, Q8N8U8, Q8NAB1, Q8NCU5
    UniProtKB/TrEMBL
    E9PFQ4
    Related
    ENSP00000377502.3, ENST00000393925.7
    Conserved Domains (5) summary
    cd14673
    Location:11421246
    PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
    pfam00169
    Location:11451241
    PH; PH domain
    pfam06008
    Location:524779
    Laminin_I; Laminin Domain I
    cl02488
    Location:583790
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
    cl19107
    Location:10361095
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
  4. NM_145753.2NP_665696.1  pleckstrin homology-like domain family B member 2 isoform c

    See identical proteins and their annotated locations for NP_665696.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC060225, AK315050, AW264132, BC069194, DA438817
    Consensus CDS
    CCDS2962.1
    UniProtKB/TrEMBL
    E9PFQ4
    Related
    ENSP00000405292.1, ENST00000412622.5
    Conserved Domains (4) summary
    cd14673
    Location:10991203
    PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
    pfam00169
    Location:11021198
    PH; PH domain
    cl02488
    Location:583747
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
    cl19107
    Location:9931062
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    111732496..111976517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    114453343..114697610
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)