PAFAH1B1 platelet activating factor acetylhydrolase 1b regulatory subunit 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PAFAH1B1provided by HGNC
Official Full Name: platelet activating factor acetylhydrolase 1b regulatory subunit 1provided by HGNC
Primary source: HGNC:HGNC:8574
See related: Ensembl:ENSG00000007168 MIM:601545; AllianceGenome:HGNC:8574
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: MDS; LIS1; LIS2; MDCR; NudF; PAFAH
Summary: This locus was identified as encoding a gene that when mutated or lost caused the lissencephaly associated with Miller-Dieker lissencephaly syndrome. This gene encodes the non-catalytic alpha subunit of the intracellular Ib isoform of platelet-activating factor acteylhydrolase, a heterotrimeric enzyme that specifically catalyzes the removal of the acetyl group at the SN-2 position of platelet-activating factor (identified as 1-O-alkyl-2-acetyl-sn-glyceryl-3-phosphorylcholine). Two other isoforms of intracellular platelet-activating factor acetylhydrolase exist: one composed of multiple subunits, the other, a single subunit. In addition, a single-subunit isoform of this enzyme is found in serum. [provided by RefSeq, Apr 2009]
Expression: Ubiquitous expression in brain (RPKM 59.5), testis (RPKM 32.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17p13.3

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (2593183..2685615)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (2482370..2574760)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (2496948..2588909)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Title: Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Lis1-dynein drives corona compaction and limits erroneous microtubule attachment at kinetochores.
Title: Lis1-dynein drives corona compaction and limits erroneous microtubule attachment at kinetochores.
NudCD1 as a prognostic marker in colorectal cancer and its role in the upregulation of cellular spindle assembly checkpoint genes and LIS1 pathways.
Title: NudCD1 as a prognostic marker in colorectal cancer and its role in the upregulation of cellular spindle assembly checkpoint genes and LIS1 pathways.
Prenatal diagnosis of Miller-Dieker syndrome/PAFAH1B1-related lissencephaly: Ultrasonography and genetically investigative results.
Title: Prenatal diagnosis of Miller-Dieker syndrome/PAFAH1B1-related lissencephaly: Ultrasonography and genetically investigative results.
Human cytomegalovirus infection is associated with increased expression of the lissencephaly gene PAFAH1B1 encoding LIS1 in neural stem cells and congenitally infected brains.
Title: Human cytomegalovirus infection is associated with increased expression of the lissencephaly gene PAFAH1B1 encoding LIS1 in neural stem cells and congenitally infected brains.
N-Acetyl-D-Glucosamine Kinase Interacts with NudC and Lis1 in Dynein Motor Complex and Promotes Cell Migration.
Title: N-Acetyl-D-Glucosamine Kinase Interacts with NudC and Lis1 in Dynein Motor Complex and Promotes Cell Migration.
Prenatal diagnosis of Miller-Dieker syndrome by chromosomal microarray.
Title: Prenatal diagnosis of Miller-Dieker syndrome by chromosomal microarray.
NudCL2 regulates cell migration by stabilizing both myosin-9 and LIS1 with Hsp90.
Title: NudCL2 regulates cell migration by stabilizing both myosin-9 and LIS1 with Hsp90.
COVID-19, microthromboses, inflammation, and platelet activating factor.
Title: COVID-19, microthromboses, inflammation, and platelet activating factor.
LIS1 binding at these sites functions in multiple stages of assembling the motile dynein-dynactin-activating adaptor complex.
Title: LIS1 promotes the formation of activated cytoplasmic dynein-1 complexes.

Submit: New GeneRIF Correction See all GeneRIFs (72)

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

Associated conditions

Description	Tests
Lissencephaly due to LIS1 mutation MedGen: C4749301 OMIM: 607432 GeneReviews: PAFAH1B1-Related Lissencephaly / Subcortical Band Heterotopia	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-10-13) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-10-13) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Inhibition of PP2A by LIS1 increases Tat mediated HIV-1 transcription	PubMed
	tat	HIV-1 Tat interacts with LIS1 in vitro and in vivo, and this interaction might contribute to the effect of Tat on microtubule formation	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-H04399 (e-PCR)
- UniSTS:35341

WI-15114 (e-PCR)
- UniSTS:25888

D17S1267 (e-PCR)
- UniSTS:149804

D17S1582 (e-PCR)
- UniSTS:152394

WI-11159 (e-PCR)
- UniSTS:63826

D17S2027 (e-PCR)
- UniSTS:77150

D17S850E (e-PCR)
- UniSTS:3456

G33155 (e-PCR)
- UniSTS:50819

STS-T60849 (e-PCR)
- UniSTS:2195

RH12602 (e-PCR)
- UniSTS:41394

D17S1798 (e-PCR)
- UniSTS:27059

RH48326 (e-PCR)
- UniSTS:91339

RH16161 (e-PCR)
- UniSTS:34261

SHGC-150914 (e-PCR)
- UniSTS:173535

RH92999 (e-PCR)
- UniSTS:86764

SHGC-130305 (e-PCR)
- UniSTS:183287

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables dynactin binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables dynein complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables dynein complex binding	IDA Inferred from Direct Assay more info	PubMed
enables dynein intermediate chain binding	IEA Inferred from Electronic Annotation more info
enables heparin binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables microtubule binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables microtubule plus-end binding	IBA Inferred from Biological aspect of Ancestor more info
enables phospholipase binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables phosphoprotein binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in JNK cascade	IEA Inferred from Electronic Annotation more info
involved_in acrosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in adult locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ameboidal-type cell migration	IEA Inferred from Electronic Annotation more info
involved_in auditory receptor cell development	IEA Inferred from Electronic Annotation more info
involved_in brain morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in brain morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cerebral cortex development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cerebral cortex neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in chemical synaptic transmission	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in cochlea development	IEA Inferred from Electronic Annotation more info
involved_in corpus callosum morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cortical microtubule organization	IEA Inferred from Electronic Annotation more info
involved_in establishment of centrosome localization	IEA Inferred from Electronic Annotation more info
involved_in establishment of mitotic spindle orientation	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of mitotic spindle orientation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of planar polarity of embryonic epithelium	IEA Inferred from Electronic Annotation more info
involved_in germ cell development	IBA Inferred from Biological aspect of Ancestor more info
involved_in hippocampus development	ISS Inferred from Sequence or Structural Similarity more info
involved_in interneuron migration	IEA Inferred from Electronic Annotation more info
involved_in layer formation in cerebral cortex	ISS Inferred from Sequence or Structural Similarity more info
involved_in learning or memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in lipid catabolic process	IEA Inferred from Electronic Annotation more info
involved_in maintenance of centrosome location	IEA Inferred from Electronic Annotation more info
involved_in microtubule cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in microtubule cytoskeleton organization involved in establishment of planar polarity	IEA Inferred from Electronic Annotation more info
involved_in microtubule organizing center organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in microtubule organizing center organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in microtubule sliding	IEA Inferred from Electronic Annotation more info
involved_in microtubule-based process	IDA Inferred from Direct Assay more info	PubMed
involved_in modulation of chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in myeloid leukocyte migration	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of JNK cascade	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in neuroblast proliferation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in neuromuscular process controlling balance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron migration	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in nuclear membrane disassembly	IEA Inferred from Electronic Annotation more info
involved_in nuclear migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in osteoclast development	IEA Inferred from Electronic Annotation more info
involved_in platelet activating factor metabolic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of axon extension	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cytokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of dendritic spine morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of embryonic development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in protein secretion	IEA Inferred from Electronic Annotation more info
involved_in radial glia-guided pyramidal neuron migration	IEA Inferred from Electronic Annotation more info
involved_in reelin-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of microtubule cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in retrograde axonal transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde axonal transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in stem cell division	IEA Inferred from Electronic Annotation more info
involved_in transmission of nerve impulse	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in vesicle transport along microtubule	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle transport along microtubule	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
part_of 1-alkyl-2-acetylglycerophosphocholine esterase complex	ISS Inferred from Sequence or Structural Similarity more info
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
located_in astral microtubule	IDA Inferred from Direct Assay more info	PubMed
located_in axon cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cell cortex	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with cell leading edge	ISS Inferred from Sequence or Structural Similarity more info
located_in central region of growth cone	IEA Inferred from Electronic Annotation more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in centrosome	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasmic microtubule	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
part_of kinesin complex	IEA Inferred from Electronic Annotation more info
is_active_in kinetochore	IBA Inferred from Biological aspect of Ancestor more info
located_in kinetochore	IDA Inferred from Direct Assay more info	PubMed
part_of microtubule associated complex	IBA Inferred from Biological aspect of Ancestor more info
part_of microtubule associated complex	IDA Inferred from Direct Assay more info	PubMed
located_in motile cilium	ISS Inferred from Sequence or Structural Similarity more info
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in neuronal cell body	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nuclear envelope	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear envelope	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in stereocilium	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: platelet-activating factor acetylhydrolase IB subunit beta

Names: lissencephaly 1 protein; platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)

NP_000421.1

EC 3.1.1.47

XP_011522203.1

EC 3.1.1.47

XP_011522204.1

EC 3.1.1.47

XP_011522205.1

EC 3.1.1.47

XP_016880190.1

EC 3.1.1.47

XP_016880192.1

EC 3.1.1.47

XP_047292118.1

EC 3.1.1.47

XP_047292119.1

EC 3.1.1.47

XP_047292120.1

EC 3.1.1.47

XP_047302781.1

EC 3.1.1.47

XP_054172273.1

EC 3.1.1.47

XP_054172274.1

EC 3.1.1.47

XP_054172275.1

EC 3.1.1.47

XP_054172276.1

EC 3.1.1.47

XP_054172277.1

EC 3.1.1.47

XP_054172278.1

EC 3.1.1.47

XP_054172279.1

EC 3.1.1.47

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.

Genomic

NG_009799.1 RefSeqGene

Range

5026..96987

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000430.4 → NP_000421.1 platelet-activating factor acetylhydrolase IB subunit beta

See identical proteins and their annotated locations for NP_000421.1

Status: REVIEWED

Source sequence(s)

AC005696, AC015799

Consensus CDS

CCDS32528.1

UniProtKB/Swiss-Prot

B2R7Q7, P43034, Q8WZ88, Q8WZ89

UniProtKB/TrEMBL

A0A6Q8PG63

Related

ENSP00000380378.4, ENST00000397195.10

Conserved Domains (3) summary

smart00667
Location:7 → 39

LisH; Lissencephaly type-1-like homology motif

cd00200
Location:104 → 408

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

sd00039
Location:111 → 148

7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

2593183..2685615

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017024701.2 → XP_016880190.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X2

UniProtKB/Swiss-Prot

B2R7Q7, P43034, Q8WZ88, Q8WZ89

UniProtKB/TrEMBL

A0A6Q8PG63

Conserved Domains (3) summary

smart00667
Location:7 → 39

LisH; Lissencephaly type-1-like homology motif

cd00200
Location:104 → 408

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

sd00039
Location:111 → 148

7WD40; WD40 repeat [structural motif]
XM_011523901.3 → XP_011522203.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X1

See identical proteins and their annotated locations for XP_011522203.1

UniProtKB/TrEMBL

A0A6Q8PFU3

Related

ENSP00000501976.1, ENST00000674608.1

Conserved Domains (4) summary

COG2319
Location:115 → 428

WD40; WD40 repeat [General function prediction only]

cd00200
Location:122 → 426

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

pfam08513
Location:30 → 53

LisH; LisH

sd00039
Location:129 → 166

7WD40; WD40 repeat [structural motif]
XM_011523902.4 → XP_011522204.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X1

See identical proteins and their annotated locations for XP_011522204.1

UniProtKB/TrEMBL

A0A6Q8PFU3

Conserved Domains (4) summary

COG2319
Location:115 → 428

WD40; WD40 repeat [General function prediction only]

cd00200
Location:122 → 426

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

pfam08513
Location:30 → 53

LisH; LisH

sd00039
Location:129 → 166

7WD40; WD40 repeat [structural motif]
XM_017024703.1 → XP_016880192.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X4
XM_047436163.1 → XP_047292119.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X2

UniProtKB/Swiss-Prot

B2R7Q7, P43034, Q8WZ88, Q8WZ89

Related

ENSP00000502843.1, ENST00000675202.1
XM_047436164.1 → XP_047292120.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X3

UniProtKB/TrEMBL

A0A6Q8PFT2

Related

ENSP00000502737.1, ENST00000676353.1
XM_047436162.1 → XP_047292118.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X2

UniProtKB/Swiss-Prot

B2R7Q7, P43034, Q8WZ88, Q8WZ89

Related

ENSP00000502031.1, ENST00000675331.1
XM_011523903.3 → XP_011522205.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X1

See identical proteins and their annotated locations for XP_011522205.1

UniProtKB/TrEMBL

A0A6Q8PFU3

Conserved Domains (4) summary

COG2319
Location:115 → 428

WD40; WD40 repeat [General function prediction only]

cd00200
Location:122 → 426

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

pfam08513
Location:30 → 53

LisH; LisH

sd00039
Location:129 → 166

7WD40; WD40 repeat [structural motif]

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

2482370..2574760

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054316303.1 → XP_054172278.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X2

UniProtKB/Swiss-Prot

B2R7Q7, P43034, Q8WZ88, Q8WZ89
XM_054316298.1 → XP_054172273.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X1

UniProtKB/TrEMBL

A0A6Q8PFU3
XM_047446825.1 → XP_047302781.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X4
XM_054316300.1 → XP_054172275.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X1

UniProtKB/TrEMBL

A0A6Q8PFU3
XM_054316302.1 → XP_054172277.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X2

UniProtKB/Swiss-Prot

B2R7Q7, P43034, Q8WZ88, Q8WZ89
XM_054316304.1 → XP_054172279.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X3

UniProtKB/TrEMBL

A0A6Q8PFT2
XM_054316301.1 → XP_054172276.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X2

UniProtKB/Swiss-Prot

B2R7Q7, P43034, Q8WZ88, Q8WZ89
XM_054316299.1 → XP_054172274.1 platelet-activating factor acetylhydrolase IB subunit beta isoform X1

UniProtKB/TrEMBL

A0A6Q8PFU3