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PDXDC1 pyridoxal dependent decarboxylase domain containing 1 [ Homo sapiens (human) ]

Gene ID: 23042, updated on 1-Jun-2020

Summary

Official Symbol
PDXDC1provided by HGNC
Official Full Name
pyridoxal dependent decarboxylase domain containing 1provided by HGNC
Primary source
HGNC:HGNC:28995
See related
Ensembl:ENSG00000179889 MIM:614244
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
LP8165
Expression
Ubiquitous expression in testis (RPKM 42.5), duodenum (RPKM 33.1) and 25 other tissues See more
Orthologs

Genomic context

See PDXDC1 in Genome Data Viewer
Location:
16p13.11
Exon count:
31
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (14974591..15153343)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15068448..15131552)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene PKD1P3-NPIPA1 readthrough Neighboring gene polycystin 1, transient receptor potential channel interacting pseudogene 3 Neighboring gene microRNA 6770-1 Neighboring gene nuclear pore complex interacting protein family member A1 Neighboring gene KIAA2013 pseudogene Neighboring gene microRNA 1972-1 Neighboring gene Sharpr-MPRA regulatory region 1947 Neighboring gene N-terminal asparagine amidase Neighboring gene RRN3 homolog, RNA polymerase I transcription factor Neighboring gene Sharpr-MPRA regulatory region 13846 Neighboring gene uncharacterized LOC100505915 Neighboring gene PKD1P6-NPIPP1 readthrough Neighboring gene nuclear pore complex interacting protein pseudogene 1 Neighboring gene microRNA 6511b-2 Neighboring gene polycystin 1, transient receptor potential channel interacting pseudogene 6 Neighboring gene microRNA 3180-4 Neighboring gene uncharacterized LOC105371096

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

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
NHGRI GWA Catalog
An atlas of genetic influences on human blood metabolites.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
NHGRI GWA Catalog
Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
NHGRI GWA Catalog
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
NHGRI GWA Catalog
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
NHGRI GWA Catalog
Human metabolic individuality in biomedical and pharmaceutical research.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0251

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cadherin binding HDA PubMed 
carboxy-lyase activity IEA
Inferred from Electronic Annotation
more info
 
pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
 
sphinganine-1-phosphate aldolase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
ameboidal-type cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
carboxylic acid metabolic process IEA
Inferred from Electronic Annotation
more info
 
sphingolipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sphingolipid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
pyridoxal-dependent decarboxylase domain-containing protein 1
NP_001272373.1
NP_001272374.1
NP_001272376.1
NP_001272377.1
NP_001272378.1
NP_001272379.1
NP_001310948.1
NP_001310949.1
NP_001310950.1
NP_055842.2
XP_005255233.1
XP_006720928.2
XP_016878548.1
XP_016878549.1
XP_016878550.1
XP_016878551.1
XP_016878552.1
XP_016878553.1
XP_016878554.1
XP_024305962.1
XP_024305963.1
XP_024305964.1
XP_024305965.1

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.

mRNA and Protein(s)

  1. NM_001285444.2NP_001272373.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001272373.1

    Status: VALIDATED

    Source sequence(s)
    AC138932, BC042104, BC053946, BC060871, BM997114, BX647809, HY036748
    Consensus CDS
    CCDS66954.1
    UniProtKB/Swiss-Prot
    Q6P996
    Related
    ENSP00000455070.1, ENST00000569715.5
    Conserved Domains (1) summary
    cl18945
    Location:145367
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  2. NM_001285445.2NP_001272374.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC138932, AK299111, BC042104, BC053946, BC060871, BM997114, D87438, HY036748
    Consensus CDS
    CCDS66955.1
    UniProtKB/Swiss-Prot
    Q6P996
    Related
    ENSP00000486662.1, ENST00000627450.2
    Conserved Domains (1) summary
    cl18945
    Location:144366
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  3. NM_001285447.1NP_001272376.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 4

    See identical proteins and their annotated locations for NP_001272376.1

    Status: VALIDATED

    Source sequence(s)
    AK295168, BC033748, BC042104, BC060871, BM997114, DA775396
    UniProtKB/Swiss-Prot
    Q6P996
    UniProtKB/TrEMBL
    B4DHL7
    Related
    ENSP00000454791.1, ENST00000563679.5
    Conserved Domains (1) summary
    cl18945
    Location:157379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  4. NM_001285448.1NP_001272377.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AK299799, BC042104, BC060871, BM997114, DA321929
    Consensus CDS
    CCDS66957.1
    UniProtKB/Swiss-Prot
    Q6P996
    Related
    ENSP00000391147.3, ENST00000450288.3
    Conserved Domains (1) summary
    cl18945
    Location:81303
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  5. NM_001285449.1NP_001272378.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 6

    See identical proteins and their annotated locations for NP_001272378.1

    Status: VALIDATED

    Source sequence(s)
    BC045554, CD370048, HY036748
    Consensus CDS
    CCDS73830.1
    UniProtKB/TrEMBL
    Q86XE2
    Related
    ENSP00000437835.2, ENST00000535621.6
    Conserved Domains (1) summary
    cl18945
    Location:172394
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  6. NM_001285450.2NP_001272379.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC138932, BC033748, BC053946, CA423507, HY036748
    Consensus CDS
    CCDS73831.1
    UniProtKB/Swiss-Prot
    Q6P996
    Related
    ENSP00000406703.2, ENST00000455313.6
    Conserved Domains (1) summary
    cl18945
    Location:172371
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  7. NM_001324019.2NP_001310948.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC138932
  8. NM_001324020.1NP_001310949.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC138932, AC139256
  9. NM_001324021.1NP_001310950.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC138932, AC139256
  10. NM_015027.4NP_055842.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_055842.2

    Status: VALIDATED

    Source sequence(s)
    AC138932, AY203955, BC042104, BC060871, BM997114, DB019664
    Consensus CDS
    CCDS32393.1
    UniProtKB/Swiss-Prot
    Q6P996
    UniProtKB/TrEMBL
    Q6XYB5
    Related
    ENSP00000379691.4, ENST00000396410.9
    Conserved Domains (1) summary
    cl18945
    Location:172394
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    14974591..15153343
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450195.1XP_024305963.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X8

    Conserved Domains (1) summary
    cl18945
    Location:190412
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  2. XM_024450194.1XP_024305962.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X7

    Conserved Domains (1) summary
    cl18945
    Location:157379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  3. XM_017023065.1XP_016878554.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6

  4. XM_017023063.1XP_016878552.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

  5. XM_017023059.1XP_016878548.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    Conserved Domains (1) summary
    cl18945
    Location:157379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  6. XM_006720865.2XP_006720928.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

    Conserved Domains (1) summary
    cl18945
    Location:130352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  7. XM_017023062.1XP_016878551.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    Conserved Domains (1) summary
    cl18945
    Location:157379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  8. XM_017023064.1XP_016878553.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

    Conserved Domains (1) summary
    cl18945
    Location:130352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  9. XM_005255176.3XP_005255233.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005255233.1

    Conserved Domains (1) summary
    cl18945
    Location:157379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  10. XM_024450196.1XP_024305964.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X9

    Conserved Domains (1) summary
    cl18945
    Location:181403
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  11. XM_017023060.1XP_016878549.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

    Conserved Domains (1) summary
    cl18945
    Location:181403
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  12. XM_017023061.2XP_016878550.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    Conserved Domains (1) summary
    cl18945
    Location:157379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...
  13. XM_024450197.1XP_024305965.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X10

    Conserved Domains (1) summary
    cl18945
    Location:130352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    523098..694938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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