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LDAF1 lipid droplet assembly factor 1 [ Homo sapiens (human) ]

Gene ID: 57146, updated on 3-Nov-2024

Summary

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Official Symbol
LDAF1provided by HGNC
Official Full Name
lipid droplet assembly factor 1provided by HGNC
Primary source
HGNC:HGNC:30136
See related
Ensembl:ENSG00000011638 MIM:611304; AllianceGenome:HGNC:30136
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
TMEM159
Summary
Involved in lipid droplet formation. Located in endoplasmic reticulum membrane and lipid droplet. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in heart (RPKM 19.6), skin (RPKM 18.8) and 23 other tissues See more
Orthologs
mouse all
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Genomic context

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See LDAF1 in Genome Data Viewer
Location:
16p12.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (21158674..21180616)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (21089598..21111555)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (21169995..21191937)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene defective in cullin neddylation 1 domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10546 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:20911499-20912284 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:20912285-20913070 Neighboring gene LYR motif containing 1 Neighboring gene dynein axonemal heavy chain 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:20982344-20983543 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:20985044-20985544 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7247 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:21059143-21059715 Neighboring gene uncharacterized LOC107984888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10547 Neighboring gene Sharpr-MPRA regulatory region 1818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:21170492-21170992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10551 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:21233480-21234004 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:21234005-21234530 Neighboring gene uncharacterized LOC105371123 Neighboring gene zona pellucida glycoprotein 2

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 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. Adipocyte-specific gene expression and adipogenic steatosis in the mouse liver due to peroxisome proliferator-activated receptor gamma1 (PPARgamma1) overexpression. Yu S, et al. J Biol Chem, 2003 Jan 3. PMID 12401792
  2. LDAF1 and Seipin Form a Lipid Droplet Assembly Complex. Chung J, et al. Dev Cell, 2019 Dec 2. PMID 31708432, Free PMC Article
  3. Promethin Is a Conserved Seipin Partner Protein. Castro IG, et al. Cells, 2019 Mar 21. PMID 30901948, Free PMC Article
  4. Identification of seipin-linked factors that act as determinants of a lipid droplet subpopulation. Eisenberg-Bord M, et al. J Cell Biol, 2018 Jan 2. PMID 29187527, Free PMC Article
  5. Identification of promethin and PGLP as two novel up-regulated genes in PPARgamma1-induced adipogenic mouse liver. Yu S, et al. Biochimie, 2004 Nov. PMID 15589683

See all (31) 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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in lipid droplet formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lipid droplet IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
lipid droplet assembly factor 1
Names
PROMETHIN
transmembrane protein 159

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_001301769.2 → NP_001288698.1  lipid droplet assembly factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001288698.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate exon in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
    Source sequence(s)
    AF001550, AF070596, AL694739, BC015812, BI821683, BX647512, CU448562
    Consensus CDS
    CCDS10595.1
    UniProtKB/Swiss-Prot
    A6NMA9, B4DEC1, O00323, Q96B96
    Related
    ENSP00000460687.1, ENST00000572599.5
    Conserved Domains (1) summary
    pfam16015
    Location:41 → 127
    Promethin; Promethin

  2. NM_001301771.2 → NP_001288700.1  lipid droplet assembly factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001288700.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
    Source sequence(s)
    AF001550, AF070596, AL694739, BC015812, BX647512, CU448562
    Consensus CDS
    CCDS10595.1
    UniProtKB/Swiss-Prot
    A6NMA9, B4DEC1, O00323, Q96B96
    Related
    ENSP00000233047.4, ENST00000233047.9
    Conserved Domains (1) summary
    pfam16015
    Location:41 → 127
    Promethin; Promethin

  3. NM_001301773.2 → NP_001288702.1  lipid droplet assembly factor 1 isoform 3

    See identical proteins and their annotated locations for NP_001288702.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 5' UTR and lacks multiple exons in the coding region, one of which results in a translational frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 5 and 6 encode the same isoform (3).
    Source sequence(s)
    AF001550, AK074667, AL694739, BX647512, CB128337, CU448562, CX786237
    Consensus CDS
    CCDS76842.1
    UniProtKB/TrEMBL
    I3L288
    Conserved Domains (1) summary
    pfam16015
    Location:41 → 89
    Promethin; Promethin

  4. NM_001301774.2 → NP_001288703.1  lipid droplet assembly factor 1 isoform 3

    See identical proteins and their annotated locations for NP_001288703.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks multiple exons in the coding region, one of which results in a translational frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 5 and 6 encode the same isoform (3).
    Source sequence(s)
    AF001550, AK074667, AL694739, BX647512, CB128337, CU448562
    Consensus CDS
    CCDS76842.1
    UniProtKB/TrEMBL
    I3L288
    Related
    ENSP00000459481.1, ENST00000572258.5
    Conserved Domains (1) summary
    pfam16015
    Location:41 → 89
    Promethin; Promethin

  5. NM_001301775.2 → NP_001288704.1  lipid droplet assembly factor 1 isoform 1

    See identical proteins and their annotated locations for NP_001288704.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF001550, AF070596, AK293557, AL694739, CU448562
    Consensus CDS
    CCDS76841.1
    Related
    ENSP00000409879.2, ENST00000451578.6
    Conserved Domains (1) summary
    pfam16015
    Location:65 → 151
    Promethin; Promethin

  6. NM_020422.6 → NP_065155.3  lipid droplet assembly factor 1 isoform 2

    See identical proteins and their annotated locations for NP_065155.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
    Source sequence(s)
    AF001550, AF070596, AK074667, AL694739, BX647512, CU448562
    Consensus CDS
    CCDS10595.1
    UniProtKB/Swiss-Prot
    A6NMA9, B4DEC1, O00323, Q96B96
    Related
    ENSP00000261388.3, ENST00000261388.7
    Conserved Domains (1) summary
    pfam16015
    Location:41 → 127
    Promethin; Promethin

RNA

  1. NR_125971.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF001550, AF070596, AK074667, AL694739, BX647512, CU448562

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    21158674..21180616
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721066.3 → XP_006721129.1  lipid droplet assembly factor 1 isoform X8

    See identical proteins and their annotated locations for XP_006721129.1

    Conserved Domains (1) summary
    pfam16015
    Location:65 → 151
    Promethin; Promethin

  2. XM_006721069.4 → XP_006721132.1  lipid droplet assembly factor 1 isoform X7

    Conserved Domains (1) summary
    pfam16015
    Location:65 → 113
    Promethin; Promethin

  3. XM_006721067.5 → XP_006721130.1  lipid droplet assembly factor 1 isoform X3

    UniProtKB/TrEMBL
    I3NI23
    Related
    ENSP00000461828.1, ENST00000573487.5
    Conserved Domains (1) summary
    pfam16015
    Location:65 → 151
    Promethin; Promethin

  4. XM_017023473.3 → XP_016878962.1  lipid droplet assembly factor 1 isoform X4

  5. XM_024450356.2 → XP_024306124.1  lipid droplet assembly factor 1 isoform X6

    Conserved Domains (1) summary
    pfam16015
    Location:41 → 127
    Promethin

  6. XM_047434370.1 → XP_047290326.1  lipid droplet assembly factor 1 isoform X5

  7. XM_024450357.2 → XP_024306125.1  lipid droplet assembly factor 1 isoform X6

    Conserved Domains (1) summary
    pfam16015
    Location:41 → 127
    Promethin

  8. XM_017023471.2 → XP_016878960.1  lipid droplet assembly factor 1 isoform X1

  9. XM_017023474.2 → XP_016878963.1  lipid droplet assembly factor 1 isoform X5

  10. XM_047434368.1 → XP_047290324.1  lipid droplet assembly factor 1 isoform X2

  11. XM_047434369.1 → XP_047290325.1  lipid droplet assembly factor 1 isoform X4

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017852933.1 Reference GRCh38.p14 PATCHES

    Range
    2486..4307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    21089598..21111555
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054313498.1 → XP_054169473.1  lipid droplet assembly factor 1 isoform X8

  2. XM_054313506.1 → XP_054169481.1  lipid droplet assembly factor 1 isoform X7

  3. XM_054313501.1 → XP_054169476.1  lipid droplet assembly factor 1 isoform X3

    UniProtKB/TrEMBL
    I3NI23

  4. XM_054313502.1 → XP_054169477.1  lipid droplet assembly factor 1 isoform X4

  5. XM_054313504.1 → XP_054169479.1  lipid droplet assembly factor 1 isoform X6

  6. XM_054313503.1 → XP_054169478.1  lipid droplet assembly factor 1 isoform X5

  7. XM_054313505.1 → XP_054169480.1  lipid droplet assembly factor 1 isoform X6

  8. XM_054313499.1 → XP_054169474.1  lipid droplet assembly factor 1 isoform X1

  9. XM_054313500.1 → XP_054169475.1  lipid droplet assembly factor 1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96B96.2 GenPept UniProtKB/Swiss-Prot:Q96B96

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