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SCP2 sterol carrier protein 2 [ Homo sapiens (human) ]

Gene ID: 6342, updated on 21-Apr-2019

Summary

Official Symbol
SCP2provided by HGNC
Official Full Name
sterol carrier protein 2provided by HGNC
Primary source
HGNC:HGNC:10606
See related
Ensembl:ENSG00000116171 MIM:184755
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
NLTP; SCPX; SCP-2; SCP-X; NSL-TP; SCP-CHI
Summary
This gene encodes two proteins: sterol carrier protein X (SCPx) and sterol carrier protein 2 (SCP2), as a result of transcription initiation from 2 independently regulated promoters. The transcript initiated from the proximal promoter encodes the longer SCPx protein, and the transcript initiated from the distal promoter encodes the shorter SCP2 protein, with the 2 proteins sharing a common C-terminus. Evidence suggests that the SCPx protein is a peroxisome-associated thiolase that is involved in the oxidation of branched chain fatty acids, while the SCP2 protein is thought to be an intracellular lipid transfer protein. This gene is highly expressed in organs involved in lipid metabolism, and may play a role in Zellweger syndrome, in which cells are deficient in peroxisomes and have impaired bile acid synthesis. Alternative splicing of this gene produces multiple transcript variants, some encoding different isoforms.[provided by RefSeq, Aug 2010]
Expression
Ubiquitous expression in liver (RPKM 77.0), duodenum (RPKM 30.8) and 24 other tissues See more
Orthologs

Genomic context

See SCP2 in Genome Data Viewer
Location:
1p32.3
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (52927229..53051617)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53392901..53517289)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene enoyl-CoA hydratase domain containing 2 Neighboring gene translation machinery-associated protein 7 pseudogene Neighboring gene ATP synthase membrane subunit 6.8PL 0pseudogene Neighboring gene RAS related 2 pseudogene Neighboring gene tubulin beta class I pseudogene 10 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 11 Neighboring gene podocan Neighboring gene solute carrier family 1 member 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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Beta-oxidation of pristanoyl-CoA, organism-specific biosystem (from REACTOME)
    Beta-oxidation of pristanoyl-CoA, organism-specific biosystemPristanoyl-CoA, generated in the peroxisome by alpha-oxidation of dietary phytanic acid, is further catabolized by three cycles of peroxisomal beta-oxidation to yield 4,8-dimethylnonanoyl-CoA, acetyl...
  • Bile acid and bile salt metabolism, organism-specific biosystem (from REACTOME)
    Bile acid and bile salt metabolism, organism-specific biosystemIn a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily. Newly synthesized bile salts are secreted into the bile and released into the small intestine where they emulsi...
  • Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate, organism-specific biosystem (from KEGG)
    Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate, organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Sterol biosynthesis
  • Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate, conserved biosystem (from KEGG)
    Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate, conserved biosystemPathway module; Carbohydrate and lipid metabolism; Sterol biosynthesis
  • DNA Damage Response (only ATM dependent), organism-specific biosystem (from WikiPathways)
    DNA Damage Response (only ATM dependent), organism-specific biosystemThis is the second pathway out of two pathways which deals with DNA damage response. It has two central gene products (ATM and TP53) which are connected with the first DNA damage response pathway. In...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Mitochondrial LC-Fatty Acid Beta-Oxidation, organism-specific biosystem (from WikiPathways)
    Mitochondrial LC-Fatty Acid Beta-Oxidation, organism-specific biosystem
    Mitochondrial LC-Fatty Acid Beta-Oxidation
  • PPAR Alpha Pathway, organism-specific biosystem (from WikiPathways)
    PPAR Alpha Pathway, organism-specific biosystemPPAR alpha (also known as NR1C1) is a nuclear receptor that is involved with transcriptional regulation of genes involved in beta-oxidation, metabolism, fatty acid transport, etc.
  • PPAR signaling pathway, organism-specific biosystem (from KEGG)
    PPAR signaling pathway, organism-specific biosystemPeroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that are activated by fatty acids and their derivatives. PPAR has three subtypes (PPARalpha, beta/delta, and gamma) s...
  • PPAR signaling pathway, conserved biosystem (from KEGG)
    PPAR signaling pathway, conserved biosystemPeroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that are activated by fatty acids and their derivatives. PPAR has three subtypes (PPARalpha, beta/delta, and gamma) s...
  • Peroxisomal beta-oxidation of tetracosanoyl-CoA, organism-specific biosystem (from WikiPathways)
    Peroxisomal beta-oxidation of tetracosanoyl-CoA, organism-specific biosystem
    Peroxisomal beta-oxidation of tetracosanoyl-CoA
  • Peroxisomal lipid metabolism, organism-specific biosystem (from REACTOME)
    Peroxisomal lipid metabolism, organism-specific biosystemIn humans, the catabolism of phytanate, pristanate, and very long chain fatty acids as well as the first four steps of the biosynthesis of plasmalogens are catalyzed by peroxisomal enzymes. Defects i...
  • Peroxisome, organism-specific biosystem (from KEGG)
    Peroxisome, organism-specific biosystemPeroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contribute to many crucial metabolic processes such as fatty acid oxidation, biosynthesis of ...
  • Peroxisome, conserved biosystem (from KEGG)
    Peroxisome, conserved biosystemPeroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contribute to many crucial metabolic processes such as fatty acid oxidation, biosynthesis of ...
  • Primary bile acid biosynthesis, organism-specific biosystem (from KEGG)
    Primary bile acid biosynthesis, organism-specific biosystemBile acids are steroid carboxylic acids derived from cholesterol in vertebrates. The primary bile acids, cholic acid and chenodeoxycholic acid, are synthesized in the liver and conjugated with taurin...
  • Primary bile acid biosynthesis, conserved biosystem (from KEGG)
    Primary bile acid biosynthesis, conserved biosystemBile acids are steroid carboxylic acids derived from cholesterol in vertebrates. The primary bile acids, cholic acid and chenodeoxycholic acid, are synthesized in the liver and conjugated with taurin...
  • Synthesis of bile acids and bile salts, organism-specific biosystem (from REACTOME)
    Synthesis of bile acids and bile salts, organism-specific biosystemIn a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily (Russell 2003). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol...
  • Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol, organism-specific biosystem (from REACTOME)
    Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol, organism-specific biosystemIn the liver, synthesis of bile acids and bile salts is initiated with the conversion of cholesterol to 7alpha-hydroxycholesterol and of 7alpha-hydroxycholesterol to 4-cholesten-7alpha-ol-3-one. The ...
  • alpha-linolenic (omega3) and linoleic (omega6) acid metabolism, organism-specific biosystem (from REACTOME)
    alpha-linolenic (omega3) and linoleic (omega6) acid metabolism, organism-specific biosystemThere are two major classes of polyunsaturated fatty acids (PUFAs): the omega-3 (n-3) and the omega-6 (n-6) fatty acids, where the number corresponds to the position of the first double bond proximat...
  • alpha-linolenic acid (ALA) metabolism, organism-specific biosystem (from REACTOME)
    alpha-linolenic acid (ALA) metabolism, organism-specific biosystemAlpha-linolenic acid (ALA, 18:3(n-3)) is an omega-3 fatty acid, supplied through diet as it cannot be synthesized by humans. ALA has an important role in human health. It is converted to long chain m...
  • bile acid biosynthesis, neutral pathway, organism-specific biosystem (from BIOCYC)
    bile acid biosynthesis, neutral pathway, organism-specific biosystemGeneral Background The biosynthesis of bile acids is a major route of : CHOLESTEROL catabolism. It converts the hydrophobic, insoluble : CHOLESTEROL molecule into soluble bile acids. Accumulation ...
  • fatty acid beta-oxidation, organism-specific biosystem (from BIOCYC)
    fatty acid beta-oxidation, organism-specific biosystemAerobic pathway Although enzymes of the pathway handle both short and long chain fatty acids, it is the long chain compounds that induce the enzymes of the pathway. Each turn of the cycle removes t...
  • fatty acid beta-oxidation (peroxisome), organism-specific biosystem (from BIOCYC)
    fatty acid beta-oxidation (peroxisome), organism-specific biosystemGeneral Background The major site for fatty acid beta-oxidation in animal cells is the mitochondrion, although partial beta-oxidation has also been shown to occur in peroxisomes. While the same sequ...
  • fatty acid beta-oxidation I, conserved biosystem (from BIOCYC)
    fatty acid beta-oxidation I, conserved biosystemThe catabolism of fatty acids proceeds via several routes, which depend on the length of the acids, whether the number of carbons is odd or even, and whether they are saturated or unsaturated. This p...
  • fatty acid beta-oxidation VI (peroxisome), conserved biosystem (from BIOCYC)
    fatty acid beta-oxidation VI (peroxisome), conserved biosystemGeneral Background The major site for fatty acid beta-oxidation in animal cells is the mitochondrion, although partial beta-oxidation has also been shown to occur in peroxisomes. Although the same s...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686C12188, DKFZp686D11188

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cholesterol binding IDA
Inferred from Direct Assay
more info
PubMed 
fatty-acyl-CoA binding IDA
Inferred from Direct Assay
more info
PubMed 
long-chain fatty acyl-CoA binding IDA
Inferred from Direct Assay
more info
PubMed 
oleic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
propanoyl-CoA C-acyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
propionyl-CoA C2-trimethyltridecanoyltransferase activity EXP
Inferred from Experiment
more info
PubMed 
propionyl-CoA C2-trimethyltridecanoyltransferase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
peroxisomal matrix TAS
Traceable Author Statement
more info
 
peroxisome IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
non-specific lipid-transfer protein
Names
epididymis secretory sperm binding protein
propanoyl-CoA C-acyltransferase
sterol carrier protein X
NP_001007099.1
NP_001007100.1
NP_001007101.1
NP_001007251.1
NP_001180528.1
NP_001180529.1
NP_001180546.1
NP_001317516.1
NP_002970.2
XP_005271160.1
XP_011540237.1

NCBI Reference Sequences (RefSeq)

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_012211.1 RefSeqGene

    Range
    4954..129342
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001007098.2NP_001007099.1  non-specific lipid-transfer protein isoform 2

    See identical proteins and their annotated locations for NP_001007099.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1. It is unknown whether this isoform (2) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AC099677, AL445183, BC067108, DC330171
    Consensus CDS
    CCDS41338.1
    UniProtKB/Swiss-Prot
    P22307
    Related
    ENSP00000360568.5, ENST00000371513.9
    Conserved Domains (1) summary
    cl27752
    Location:12317
    PRK06064; acetyl-CoA acetyltransferase; Provisional
  2. NM_001007099.2NP_001007100.1  non-specific lipid-transfer protein isoform 5 precursor

    See identical proteins and their annotated locations for NP_001007100.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) results from transcription initiation from a downstream promoter. This variant (3) 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, also known as SCP2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AA664009, AB208789, BC005911, M55421
    Consensus CDS
    CCDS44149.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000396413.2, ENST00000435345.6
    Conserved Domains (1) summary
    pfam02036
    Location:48134
    SCP2; SCP-2 sterol transfer family
  3. NM_001007100.2NP_001007101.1  non-specific lipid-transfer protein isoform 4

    See identical proteins and their annotated locations for NP_001007101.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) results from transcription initiation from a downstream promoter. This variant (4) 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 (4) has a distinct N-terminus and is shorter than isoform 1. It is unknown whether this isoform (4) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, DB459183, M55421
    Consensus CDS
    CCDS44150.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000406636.2, ENST00000430330.6
    Conserved Domains (1) summary
    pfam02036
    Location:45131
    SCP2; SCP-2 sterol transfer family
  4. NM_001007250.2NP_001007251.1  non-specific lipid-transfer protein isoform 3

    See identical proteins and their annotated locations for NP_001007251.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) results from transcription initiation from a downstream promoter. 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 (3) has a distinct N-terminus and is shorter than isoform 1. It is unknown whether this isoform (3) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, CA867670, M55421
    Consensus CDS
    CCDS30719.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000386214.3, ENST00000408941.7
  5. NM_001193599.1NP_001180528.1  non-specific lipid-transfer protein isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (7) is shorter than isoform 1. It is unknown whether this isoform (7) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, AC099677, AK294631, AL445183, DC330171
    Consensus CDS
    CCDS53318.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000384569.2, ENST00000407246.6
    Conserved Domains (3) summary
    PRK08256
    Location:12380
    PRK08256; lipid-transfer protein; Provisional
    cd00826
    Location:17379
    nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...
    pfam02036
    Location:428514
    SCP2; SCP-2 sterol transfer family
  6. NM_001193600.1NP_001180529.1  non-specific lipid-transfer protein isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (6) is shorter than isoform 1. It is unknown whether this isoform (6) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, AC099677, AK308105, AL445183, DC330171
    Consensus CDS
    CCDS53317.1
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000360564.4, ENST00000371509.8
    Conserved Domains (3) summary
    PRK08256
    Location:12360
    PRK08256; lipid-transfer protein; Provisional
    pfam02036
    Location:408494
    SCP2; SCP-2 sterol transfer family
    cl09938
    Location:17359
    cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
  7. NM_001193617.1NP_001180546.1  non-specific lipid-transfer protein isoform 8

    See identical proteins and their annotated locations for NP_001180546.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) 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 (8) has a shorter N-terminus, compared to isoform 1. It is unknown whether this isoform (8) is proteolytically processed like isoforms 1 and 5.
    Source sequence(s)
    AA664009, AB208789, AC099677, AK295214, DC330171
    Consensus CDS
    CCDS53319.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    Q59HG9
    Related
    ENSP00000434132.1, ENST00000528311.5
    Conserved Domains (2) summary
    pfam02036
    Location:371457
    SCP2; SCP-2 sterol transfer family
    cl09938
    Location:1322
    cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
  8. NM_001330587.1NP_001317516.1  non-specific lipid-transfer protein isoform 9

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (9) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC099677, AL445183
    Consensus CDS
    CCDS81325.1
    UniProtKB/TrEMBL
    E9PLD1
    Related
    ENSP00000491562.1, ENST00000640998.1
  9. NM_002979.5NP_002970.2  non-specific lipid-transfer protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_002970.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as SCPx).
    Source sequence(s)
    AA664009, AB208789, AK312856, AL445183, DC330171
    Consensus CDS
    CCDS572.1
    UniProtKB/Swiss-Prot
    P22307
    UniProtKB/TrEMBL
    B2R761, Q59HG9
    Related
    ENSP00000360569.3, ENST00000371514.8
    Conserved Domains (2) summary
    PRK08256
    Location:12404
    PRK08256; lipid-transfer protein; Provisional
    pfam02036
    Location:452538
    SCP2; SCP-2 sterol transfer family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    52927229..53051617
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005271103.4XP_005271160.1  non-specific lipid-transfer protein isoform X1

    See identical proteins and their annotated locations for XP_005271160.1

    Conserved Domains (2) summary
    PRK08256
    Location:12404
    PRK08256; lipid-transfer protein; Provisional
    cd00826
    Location:17403
    nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...
  2. XM_011541935.2XP_011540237.1  non-specific lipid-transfer protein isoform X2

    Conserved Domains (2) summary
    COG0183
    Location:12374
    PaaJ; Acetyl-CoA acetyltransferase [Lipid transport and metabolism]
    cd00826
    Location:17380
    nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...
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