Ccdc39 coiled-coil domain 39 molecular ruler complex subunit [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ccdc39provided by RGD
Official Full Name: coiled-coil domain 39 molecular ruler complex subunitprovided by RGD
Primary source: RGD:1306277
See related: EnsemblRapid:ENSRNOG00000011440 AllianceGenome:RGD:1306277
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
Also known as: RGD1306277
Summary: Predicted to be involved in several processes, including cilium-dependent cell motility; determination of left/right symmetry; and inner dynein arm assembly. Predicted to act upstream of or within several processes, including cerebrospinal fluid circulation; establishment of left/right asymmetry; and regulation of cilium beat frequency. Predicted to be located in 9+2 motile cilium and cytosol. Predicted to be active in axoneme. Used to study hydrocephalus. Human ortholog(s) of this gene implicated in primary ciliary dyskinesia 14. Orthologous to human CCDC39 (coiled-coil domain 39 molecular ruler complex subunit). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 186.2), Spleen (RPKM 171.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q24

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (118593881..118631584, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (116665651..116703354, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (120278605..120367829, complement)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

in Ccdc39(prh/prh) mutant rats demonstrate a possible causal role of neuroinflammation in neonatal hydrocephalus development, which involves impaired cortical development and glymphatic CSF flow.
Title: Impaired neural differentiation and glymphatic CSF flow in the Ccdc39 rat model of neonatal hydrocephalus: genetic interaction with L1cam.

Submit: New GeneRIF Correction

General gene information

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Markers

BF388236 (e-PCR)
- UniSTS:244875

RH134053 (e-PCR)
- UniSTS:217335

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in axonemal dynein complex assembly	ISO Inferred from Sequence Orthology more info
involved_in axonemal dynein complex assembly	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebrospinal fluid circulation	ISO Inferred from Sequence Orthology more info
involved_in cilium movement	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cilium movement	ISO Inferred from Sequence Orthology more info
involved_in cilium-dependent cell motility	IBA Inferred from Biological aspect of Ancestor more info
involved_in cilium-dependent cell motility	ISO Inferred from Sequence Orthology more info
involved_in cilium-dependent cell motility	ISS Inferred from Sequence or Structural Similarity more info
involved_in determination of digestive tract left/right asymmetry	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within determination of left/right symmetry	ISO Inferred from Sequence Orthology more info
involved_in determination of liver left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in determination of pancreatic left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in epithelial cilium movement involved in determination of left/right asymmetry	IBA Inferred from Biological aspect of Ancestor more info
involved_in epithelial cilium movement involved in determination of left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in epithelial cilium movement involved in determination of left/right asymmetry	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within epithelial cilium movement involved in extracellular fluid movement	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of left/right asymmetry	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within flagellated sperm motility	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
involved_in heart looping	ISO Inferred from Sequence Orthology more info
involved_in inner dynein arm assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in inner dynein arm assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inner dynein arm assembly	ISO Inferred from Sequence Orthology more info
involved_in lung development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within motile cilium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization to cilium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cilium beat frequency	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in 9+2 motile cilium	ISO Inferred from Sequence Orthology more info
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
located_in axoneme	IEA Inferred from Electronic Annotation more info
located_in axoneme	ISO Inferred from Sequence Orthology more info
located_in axoneme	ISS Inferred from Sequence or Structural Similarity more info
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: coiled-coil domain-containing protein 39

Names: coiled-coil domain containing 39

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_001415040.1 → NP_001401969.1 coiled-coil domain-containing protein 39

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/Swiss-Prot

D3Z8K2, D4A2M2

Related

ENSRNOP00000069773.1, ENSRNOT00000084521.3

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_086020.1 Reference GRCr8

Range

118593881..118631584 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001107667.1: Suppressed sequence

Description

NM_001107667.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.