Psd4 MGI Mouse Gene Detail - MGI:2674093 - pleckstrin and Sec7 domain containing 4

Symbol

Psd4
Name

pleckstrin and Sec7 domain containing 4
Synonyms

EFA6B, SEC7 homolog

Feature Type

protein coding gene
IDs

MGI:2674093
NCBI Gene: 215632
Alliance

gene page
Transcription Start Sites

11 TSS

Sequence Map

Chr2:24257571-24299882 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 16.38 cM
Mapping Data

2 experiments

SNPs within 2kb

1308 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2674093	protein coding gene	Chr2:24257571-24304966 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0025409	protein coding gene	Chr2:22172166-22221617 (+)
A/J	MGP_AJ_G0025386	protein coding gene	Chr2:21314043-21362303 (+)
AKR/J	MGP_AKRJ_G0025356	protein coding gene	Chr2:22045581-22094242 (+)
BALB/cJ	MGP_BALBcJ_G0025382	protein coding gene	Chr2:21422256-21471604 (+)
C3H/HeJ	MGP_C3HHeJ_G0025143	protein coding gene	Chr2:21980691-22028067 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0025826	protein coding gene	Chr2:22878619-22927061 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023237	protein coding gene	Chr2:20241682-20289166 (+)
CAST/EiJ	MGP_CASTEiJ_G0024606	protein coding gene	Chr2:21815050-21865478 (+)
CBA/J	MGP_CBAJ_G0025121	protein coding gene	Chr2:23683838-23732230 (+)
DBA/2J	MGP_DBA2J_G0025254	protein coding gene	Chr2:21171607-21220762 (+)
FVB/NJ	MGP_FVBNJ_G0025216	protein coding gene	Chr2:20911504-20961492 (+)
LP/J	MGP_LPJ_G0025340	protein coding gene	Chr2:22103589-22158150 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025247	protein coding gene	Chr2:23921151-23970888 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025885	protein coding gene	Chr2:21972283-22024391 (+)
PWK/PhJ	MGP_PWKPhJ_G0024354	protein coding gene	Chr2:20956644-21003369 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0024154	protein coding gene	Chr2:22094839-22143128 (+)
WSB/EiJ	MGP_WSBEiJ_G0024675	protein coding gene	Chr2:22043058-22091504 (+)

Human Ortholog

PSD4, pleckstrin and Sec7 domain containing 4

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PSD4, pleckstrin and Sec7 domain containing 4
Synonyms

EFA6B, TIC
Links

HGNC:19096

NCBI Gene ID: 23550

neXtProt AC: NX_Q8NDX1

UniProt: Q8NDX1
Chr Location

2q14.1; chr2:113157325-113209396 (+) GRCh38

MGI Vertebrate Homology

Psd4 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: PSD4
Gene Tree

Psd4

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Phenotype Summary

1 phenotype from 1 allele in 1 genetic background
9 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

6
Endonuclease-mediated

1
Gene trapped

1
Targeted

4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

39 strains or lines available

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All GO Annotations

7
GO References

6

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

850
Tissues

25
cDNA Data

14
Literature Summary

4

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase psd4

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All Sequences

82
RefSeq

24
UniProt

6
CCDS

CCDS15737.1

Ensembl

ENSMUSG00000026979 (Evidence)
NCBI Gene

215632

			Length	Strain/Species	Flank
genomic	215632	NCBI Gene Model \| MGI Sequence Detail	42312	C57BL/6J	± kb
transcript	NM_001355231	RefSeq \| MGI Sequence Detail	5484	C57BL/6
polypeptide	Q8BLR5	UniProt \| EBI \| MGI Sequence Detail	1005	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000013343 PH and SEC7 domain-containing protein 4

(term hierarchy)
InterPro Domains

IPR011993 PH-like domain superfamily

IPR001849 Pleckstrin homology domain

IPR041681 Pleckstrin homology domain 9

IPR023394 Sec7, C-terminal domain superfamily

IPR000904 Sec7 domain

IPR035999 Sec7 domain superfamily
GlyGen

Q8BLR5 1 site, 1 N-linked glycan (1 site)

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All nucleic 15

cDNA 14

Primer pair 1

Microarray probesets 5

Summaries

All 37

Developmental Gene Expression 4

Gene Ontology 6

Phenotypes 9
Earliest

J:82808 Strausberg RL, et al., Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Psd4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr16617	Chr2:24257577-24257632 (+)	34 bp
Tssr16618	Chr2:24269133-24269136 (+)	11,564 bp
Tssr16619	Chr2:24275143-24275179 (+)	17,590 bp
Tssr16620	Chr2:24275325-24275364 (+)	17,774 bp
Tssr16621	Chr2:24275365-24275370 (+)	17,797 bp
Tssr16622	Chr2:24276345-24276381 (+)	18,792 bp
Tssr16623	Chr2:24276387-24276398 (+)	18,822 bp
Tssr16624	Chr2:24276545-24276554 (+)	18,979 bp
Tssr16625	Chr2:24276616-24276640 (+)	19,057 bp
Tssr16626	Chr2:24276650-24276664 (+)	19,086 bp
Tssr16627	Chr2:24284802-24284820 (+)	27,240 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/12/2024 MGI 6.24