Ttc21b tetratricopeptide repeat domain 21B [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Ttc21bprovided by RGD
Full Name: tetratricopeptide repeat domain 21Bprovided by RGD
Primary source: RGD:1565122
See related: Ensembl:ENSRNOG00000005868 AllianceGenome:RGD:1565122
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: RGD1565122
Summary: Predicted to enable chromatin binding activity. Predicted to be involved in intraciliary retrograde transport; protein localization to cilium; and regulation of intraciliary retrograde transport. Predicted to act upstream of or within several processes, including central nervous system development; regulation of gene expression; and regulation of signal transduction. Predicted to be located in cilium. Predicted to be part of intraciliary transport particle A. Human ortholog(s) of this gene implicated in asphyxiating thoracic dystrophy 4 and nephronophthisis 12. Orthologous to human TTC21B (tetratricopeptide repeat domain 21B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 203.2), Kidney (RPKM 188.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q21

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (71269425..71343936, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (50861367..50935880, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (52286794..52361060, complement)

Chromosome 3 - NC_086021.1 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?

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chromatin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within Bergmann glial cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellar Purkinje cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellum development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
involved_in intraciliary retrograde transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intraciliary retrograde transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of eating behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in protein localization to cilium	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein localization to cilium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization to non-motile cilium	ISO Inferred from Sequence Orthology more info
involved_in regulation of intraciliary retrograde transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular system development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cilium	IEA Inferred from Electronic Annotation more info
part_of intraciliary transport particle A	IBA Inferred from Biological aspect of Ancestor more info
part_of intraciliary transport particle A	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: tetratricopeptide repeat protein 21B

Names: tetratricopeptide repeat protein 21B-like

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_001191737.2 → NP_001178666.1 tetratricopeptide repeat protein 21B

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

D4A333

Related

ENSRNOP00000083967.1, ENSRNOT00000118540.1

Conserved Domains (4) summary

sd00006
Location:883 → 911

TPR; TPR repeat [structural motif]

pfam00515
Location:721 → 754

TPR_1; Tetratricopeptide repeat

pfam13414
Location:720 → 783

TPR_11; TPR repeat

pfam14559
Location:895 → 960

TPR_19; Tetratricopeptide repeat

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_086021.1 Reference GRCr8

Range

71269425..71343936 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039104488.2 → XP_038960416.1 tetratricopeptide repeat protein 21B isoform X1

UniProtKB/TrEMBL

D4A333

Conserved Domains (2) summary

TIGR02917
Location:242 → 1052

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:633 → 661

TPR; TPR repeat [structural motif]