Pdxdc1 pyridoxal-dependent decarboxylase domain containing 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pdxdc1provided by MGI
Official Full Name: pyridoxal-dependent decarboxylase domain containing 1provided by MGI
Primary source: MGI:MGI:1920909
See related: Ensembl:ENSMUSG00000022680 AllianceGenome:MGI:1920909
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Kiaa0251-hp; 2210010A19Rik
Summary: Predicted to enable carboxy-lyase activity and pyridoxal phosphate binding activity. Predicted to be involved in carboxylic acid metabolic process. Predicted to be located in Golgi apparatus. Predicted to be active in intracellular membrane-bounded organelle. Is expressed in central nervous system and retina. Orthologous to several human genes including PDXDC1 (pyridoxal dependent decarboxylase domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in testis adult (RPKM 34.6), colon adult (RPKM 34.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 A1; 16 9.64 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (13651025..13721018, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (13833145..13903176, complement)

Chromosome 16 - NC_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of PDXDC1 as a novel pleiotropic susceptibility locus shared between lumbar spine bone mineral density and birth weight.
Title: Identification of PDXDC1 as a novel pleiotropic susceptibility locus shared between lumbar spine bone mineral density and birth weight.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH124466 (e-PCR)
- UniSTS:161288

44.MMHAP75FRG11.seq (e-PCR)
- UniSTS:124549

Ntan1 (e-PCR), detects polymorphism
- UniSTS:144070

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables carboxy-lyase activity	IEA Inferred from Electronic Annotation more info
enables pyridoxal phosphate binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in carboxylic acid metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: pyridoxal-dependent decarboxylase domain-containing protein 1

NP_001034622.1

EC 4.1.1.-

NP_001277946.1

EC 4.1.1.-

NP_001344154.1

EC 4.1.1.-

NP_444411.2

EC 4.1.1.-

XP_011244355.1

EC 4.1.1.-

XP_011244356.1

EC 4.1.1.-

XP_011244357.1

EC 4.1.1.-

XP_036016092.1

EC 4.1.1.-

XP_036016093.1

EC 4.1.1.-

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)

NM_001039533.2 → NP_001034622.1 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 3

See identical proteins and their annotated locations for NP_001034622.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an internal exon in the 3' coding region, which results in a frameshift, compared to variant 4. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 4.

Source sequence(s)

AC107769, AK004611, AK054329

Consensus CDS

CCDS37261.1

UniProtKB/Swiss-Prot

Q99K01

Related

ENSMUSP00000111471.3, ENSMUST00000115804.9

Conserved Domains (1) summary

cl18945
Location:172 → 394

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 ...
NM_001291017.1 → NP_001277946.1 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 4

See identical proteins and their annotated locations for NP_001277946.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) encodes the longest isoform (4).

Source sequence(s)

AC107769, AK054329

Consensus CDS

CCDS70685.1

UniProtKB/TrEMBL

A0A0R4J034

Related

ENSMUSP00000023361.6, ENSMUST00000023361.12

Conserved Domains (1) summary

cl18945
Location:172 → 394

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 ...
NM_001357225.1 → NP_001344154.1 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 5

Status: VALIDATED

Source sequence(s)

AC107769

Conserved Domains (1) summary

cl18945
Location:171 → 393

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 ...
NM_053181.3 → NP_444411.2 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_444411.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) lacks the terminal exon used in variant 4 and its 3' terminal exon extends past a splice site that is used in variant 4. This results in a novel 3' coding region and 3' UTR, compared to variant 4. It encodes isoform 1 which is shorter and has a distinct C-terminus, compared to isoform 4.

Source sequence(s)

AC107769, AK030613, AK033107, AK054329, BY469248

UniProtKB/Swiss-Prot

Q3TCL3, Q3TN13, Q8BMK9, Q8BW02, Q8BW51, Q8BZZ4, Q99K01, Q9DC25

Related

ENSMUST00000154150.8

Conserved Domains (1) summary

cl18945
Location:172 → 394

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: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

13651025..13721018 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011246054.4 → XP_011244356.1 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

Conserved Domains (1) summary

cl18945
Location:171 → 393

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 ...
XM_011246053.3 → XP_011244355.1 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

Conserved Domains (1) summary

cl18945
Location:172 → 394

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 ...
XM_011246055.4 → XP_011244357.1 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

Conserved Domains (1) summary

cl18945
Location:150 → 372

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 ...
XM_036160199.1 → XP_036016092.1 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

Conserved Domains (1) summary

cl18945
Location:171 → 393

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 ...
XM_036160200.1 → XP_036016093.1 pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

Conserved Domains (1) summary

cl18945
Location:172 → 394

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 ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_178853.2: Suppressed sequence

Description

NM_178853.2: This RefSeq was temporarily suppressed because the splicing pattern of AK075829.1, which was used as its source, does not occur in any other transcripts.