Ift172 intraflagellar transport 172 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ift172provided by RGD
Official Full Name: intraflagellar transport 172provided by RGD
Primary source: RGD:620744
See related: EnsemblRapid:ENSRNOG00000057813 AllianceGenome:RGD:620744
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: Slb
Summary: Involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in sperm cytoplasmic droplet; sperm midpiece; and sperm principal piece. Predicted to be part of intraciliary transport particle B. Predicted to be active in axoneme and ciliary basal body. Human ortholog(s) of this gene implicated in Bardet-Biedl syndrome 20; retinitis pigmentosa 71; and short-rib thoracic dysplasia 10 with or without polydactyly. Orthologous to human IFT172 (intraflagellar transport 172). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Testes (RPKM 121.0), Kidney (RPKM 76.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q14

Exon count:: 49

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (30801841..30841239)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (25081933..25121271)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (26390686..26485459)

Chromosome 6 - NC_086024.1 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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Markers

RH134643 (e-PCR)
- UniSTS:217922

RH131827 (e-PCR)
- UniSTS:215110

RH143087 (e-PCR)
- UniSTS:232334

RH92034 (e-PCR)
- UniSTS:87789

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in Notch signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Notch signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in bone development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within bone development	ISO Inferred from Sequence Orthology more info
involved_in brain development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in cytoplasmic microtubule organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cytoplasmic microtubule organization	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 dorsal/ventral pattern formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
involved_in embryonic camera-type eye morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic camera-type eye morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in epidermis development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within epidermis development	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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within heart looping	ISO Inferred from Sequence Orthology more info
involved_in hindgut development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within hindgut development	ISO Inferred from Sequence Orthology more info
involved_in intraciliary transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in left/right axis specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within left/right axis specification	ISO Inferred from Sequence Orthology more info
involved_in limb development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within limb development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neural tube closure	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube formation	ISO Inferred from Sequence Orthology more info
involved_in non-motile cilium assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within non-motile cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in protein processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein processing	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in roof of mouth development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within roof of mouth development	ISO Inferred from Sequence Orthology more info
involved_in smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in spinal cord motor neuron differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within spinal cord motor neuron differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
is_active_in ciliary basal body	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	IEA Inferred from Electronic Annotation more info
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cilium	ISS Inferred from Sequence or Structural Similarity more info
part_of intraciliary transport particle B	IBA Inferred from Biological aspect of Ancestor more info
part_of intraciliary transport particle B	IEA Inferred from Electronic Annotation more info
part_of intraciliary transport particle B	ISO Inferred from Sequence Orthology more info
part_of intraciliary transport particle B	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in sperm cytoplasmic droplet	IEA Inferred from Electronic Annotation more info
located_in sperm cytoplasmic droplet	ISO Inferred from Sequence Orthology more info
located_in sperm midpiece	IEA Inferred from Electronic Annotation more info
located_in sperm midpiece	ISO Inferred from Sequence Orthology more info
located_in sperm principal piece	IEA Inferred from Electronic Annotation more info
located_in sperm principal piece	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: intraflagellar transport protein 172 homolog

Names: intraflagellar transport 172 homolog; selective LIM binding factor homolog; selective LIM binding factor, rat homolog; selective LIM-binding factor

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_001434132.1 → NP_001421061.1 intraflagellar transport protein 172 homolog

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/Swiss-Prot

Q9JKU3

UniProtKB/TrEMBL

A0A096MJL0

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_086024.1 Reference GRCr8

Range

30801841..30841239

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039111607.2 → XP_038967535.1 intraflagellar transport protein 172 homolog isoform X1

Related

ENSRNOP00000069468.3, ENSRNOT00000091528.3

Conserved Domains (4) summary

cd15832
Location:810 → 866

SNAP; TPR repeat [structural motif]

sd00039
Location:20 → 64

7WD40; WD40 repeat [structural motif]

cl24038
Location:810 → 994

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family

cl29593
Location:17 → 318

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 ...
XM_039111609.1 → XP_038967537.1 intraflagellar transport protein 172 homolog isoform X2

UniProtKB/Swiss-Prot

Q9JKU3

Conserved Domains (2) summary

cd15832
Location:634 → 690

SNAP; TPR repeat [structural motif]

cl24038
Location:634 → 818

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
XM_039111610.2 → XP_038967538.1 intraflagellar transport protein 172 homolog isoform X3

UniProtKB/TrEMBL

A6HA62

Conserved Domains (2) summary

cd15832
Location:290 → 346

SNAP; TPR repeat [structural motif]

cl24038
Location:290 → 474

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_053792.2: Suppressed sequence

Description

NM_053792.2: This RefSeq was removed because currently there is insufficient support for the transcript.