Plekhm1 pleckstrin homology and RUN domain containing M1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Plekhm1provided by RGD
Official Full Name: pleckstrin homology and RUN domain containing M1provided by RGD
Primary source: RGD:1308010
See related: EnsemblRapid:ENSRNOG00000028521 AllianceGenome:RGD:1308010
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including autophagosome-lysosome fusion; positive regulation of bone resorption; and positive regulation of ruffle assembly. Predicted to be located in autolysosome and nucleolus. Human ortholog(s) of this gene implicated in autosomal recessive osteopetrosis 6 and osteopetrosis. Orthologous to human PLEKHM1 (pleckstrin homology and RUN domain containing M1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Adrenal (RPKM 107.1), Spleen (RPKM 66.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q32.1

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (88814699..88876570, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (88313837..88366182, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (91451890..91500675, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in autophagosome-lysosome fusion	ISO Inferred from Sequence Orthology more info
involved_in autophagosome-lysosome fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in late endosome to lysosome transport	ISO Inferred from Sequence Orthology more info
involved_in late endosome to lysosome transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in lysosome localization	ISO Inferred from Sequence Orthology more info
involved_in lysosome localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of bone resorption	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of bone resorption	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of ruffle assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ruffle assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in autolysosome	ISO Inferred from Sequence Orthology more info
located_in autolysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in autolysosome membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in late endosome	IEA Inferred from Electronic Annotation more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: pleckstrin homology domain-containing family M member 1

Names: PH domain-containing family M member 1; pleckstrin homology domain containing, family M (with RUN domain) member 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_001009677.3 → NP_001009677.1 pleckstrin homology domain-containing family M member 1

See identical proteins and their annotated locations for NP_001009677.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

Q5PQS0

UniProtKB/TrEMBL

A0A8I6AI11

Related

ENSRNOP00000034752.4, ENSRNOT00000037147.7

Conserved Domains (4) summary

smart00233
Location:688 → 780

PH; Pleckstrin homology domain

cd13321
Location:508 → 631

PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain

pfam02759
Location:48 → 179

RUN; RUN domain

pfam13901
Location:850 → 1048

zf-RING_9; Putative zinc-RING and/or ribbon

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

88814699..88876570 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039086121.2 → XP_038942049.1 pleckstrin homology domain-containing family M member 1 isoform X1

Conserved Domains (4) summary

smart00233
Location:688 → 780

PH; Pleckstrin homology domain

cd13321
Location:508 → 631

PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain

pfam02759
Location:48 → 179

RUN; RUN domain

pfam13901
Location:850 → 1048

zf-RING_9; Putative zinc-RING and/or ribbon
XM_008768292.3 → XP_008766514.1 pleckstrin homology domain-containing family M member 1 isoform X3

UniProtKB/TrEMBL

A0A8I6AI11

Related

ENSRNOP00000106445.1, ENSRNOT00000150646.1

Conserved Domains (6) summary

smart00233
Location:600 → 692

PH; Pleckstrin homology domain

cd13321
Location:420 → 543

PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain

pfam00169
Location:449 → 538

PH; PH domain

pfam02759
Location:5 → 93

RUN; RUN domain

pfam13901
Location:761 → 963

zf-RING_9; Putative zinc-RING and/or ribbon

pfam15265
Location:132 → 310

FAM196; FAM196 family
XM_006247527.4 → XP_006247589.1 pleckstrin homology domain-containing family M member 1 isoform X2

UniProtKB/TrEMBL

A0A8I6AI11

Conserved Domains (6) summary

smart00233
Location:640 → 732

PH; Pleckstrin homology domain

cd13321
Location:460 → 583

PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain

pfam00169
Location:489 → 578

PH; PH domain

pfam02759
Location:1 → 133

RUN; RUN domain

pfam13901
Location:801 → 1003

zf-RING_9; Putative zinc-RING and/or ribbon

pfam15265
Location:172 → 350

FAM196; FAM196 family
XM_063269179.1 → XP_063125249.1 pleckstrin homology domain-containing family M member 1 isoform X2

UniProtKB/TrEMBL

A0A8I6AI11

Related

ENSRNOP00000093121.1, ENSRNOT00000116440.2