Ift122 intraflagellar transport 122 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ift122provided by RGD
Official Full Name: intraflagellar transport 122provided by RGD
Primary source: RGD:1311302
See related: EnsemblRapid:ENSRNOG00000010952 AllianceGenome:RGD:1311302
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: Wdr10
Summary: Predicted to be involved in several processes, including cilium organization; embryonic morphogenesis; and protein localization to organelle. Predicted to act upstream of or within several processes, including embryonic morphogenesis; negative regulation of smoothened signaling pathway; and smoothened signaling pathway. Predicted to be located in several cellular components, including ciliary basal body; ciliary base; and photoreceptor connecting cilium. Predicted to be part of intraciliary transport particle A. Predicted to be active in non-motile cilium. Human ortholog(s) of this gene implicated in cranioectodermal dysplasia 1. Orthologous to human IFT122 (intraflagellar transport 122). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 165.6), Kidney (RPKM 89.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q42

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (150577525..150648052)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (148905031..148975458)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (147756574..147826983)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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 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

Process	Evidence Code	Pubs
involved_in camera-type eye morphogenesis	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
acts_upstream_of_or_within dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
involved_in embryonic body morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic camera-type eye morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic digit morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic heart tube development	ISO Inferred from Sequence Orthology more info
involved_in embryonic heart tube left/right pattern formation	ISO Inferred from Sequence Orthology more info
involved_in establishment of protein localization to organelle	ISO Inferred from Sequence Orthology more info
involved_in intracellular signal transduction	ISO Inferred from Sequence Orthology more info
involved_in intraciliary anterograde transport	ISO Inferred from Sequence Orthology more info
involved_in intraciliary retrograde transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intraciliary retrograde transport	ISO Inferred from Sequence Orthology more info
involved_in intraciliary transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in limb development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of keratinocyte proliferation	ISO Inferred from Sequence Orthology 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 smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in neural tube closure	ISO Inferred from Sequence Orthology more info
involved_in non-motile cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within non-motile cilium assembly	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
involved_in protein localization to cilium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within receptor clustering	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within smoothened signaling pathway involved in dorsal/ventral neural tube patterning	ISO Inferred from Sequence Orthology more info
involved_in spinal cord dorsal/ventral patterning	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
located_in ciliary base	ISO Inferred from Sequence Orthology more info
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology 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
is_active_in non-motile cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in photoreceptor connecting cilium	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: intraflagellar transport protein 122 homolog

Names: WD repeat domain 10; intraflagellar transport 122 homolog

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_001009416.2 → NP_001009416.1 intraflagellar transport protein 122 homolog isoform 2

See identical proteins and their annotated locations for NP_001009416.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A0A8J8XQ65, F1M7W3, Q5PPJ1

Conserved Domains (3) summary

COG2319
Location:15 → 289

WD40; WD40 repeat [General function prediction only]

sd00039
Location:15 → 51

7WD40; WD40 repeat [structural motif]

cl02567
Location:49 → 291

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 ...
NM_001309521.1 → NP_001296450.1 intraflagellar transport protein 122 homolog isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A0A8I5ZMU0

Related

ENSRNOP00000086252.2, ENSRNOT00000112295.2

Conserved Domains (5) summary

COG2319
Location:15 → 289

WD40; WD40 repeat [General function prediction only]

cd15832
Location:646 → 701

SNAP; TPR repeat [structural motif]

sd00039
Location:15 → 51

7WD40; WD40 repeat [structural motif]

cl02567
Location:49 → 291

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 ...

cl24038
Location:641 → 831

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

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_086022.1 Reference GRCr8

Range

150577525..150648052

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063286092.1 → XP_063142162.1 intraflagellar transport protein 122 homolog isoform X1

UniProtKB/TrEMBL

A0A8I5ZMU0
XM_039107640.2 → XP_038963568.1 intraflagellar transport protein 122 homolog isoform X3

UniProtKB/TrEMBL

A0A8I5ZMU0

Conserved Domains (3) summary

TIGR02917
Location:710 → 953

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00039
Location:15 → 51

7WD40; WD40 repeat [structural motif]

cl29593
Location:12 → 190

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_063286093.1 → XP_063142163.1 intraflagellar transport protein 122 homolog isoform X2

UniProtKB/TrEMBL

A0A8I5ZMU0
XM_006237067.4 → XP_006237129.1 intraflagellar transport protein 122 homolog isoform X4

See identical proteins and their annotated locations for XP_006237129.1

UniProtKB/TrEMBL

A0A0G2JZL6, A0A8I5ZMU0, A6IL02

Related

ENSRNOP00000071095.1, ENSRNOT00000086549.3

Conserved Domains (5) summary

COG2319
Location:4 → 348

WD40; WD40 repeat [General function prediction only]

cd15832
Location:705 → 760

SNAP; TPR repeat [structural motif]

sd00039
Location:15 → 51

7WD40; WD40 repeat [structural motif]

cl02567
Location:12 → 190

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 ...

cl24038
Location:700 → 890

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
XM_063286094.1 → XP_063142164.1 intraflagellar transport protein 122 homolog isoform X5

UniProtKB/TrEMBL

A0A8I5ZMU0
XM_039107642.2 → XP_038963570.1 intraflagellar transport protein 122 homolog isoform X7

UniProtKB/TrEMBL

A0A8I5ZMU0, A0A8I6A5N4

Conserved Domains (3) summary

TIGR02917
Location:651 → 894

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00039
Location:15 → 51

7WD40; WD40 repeat [structural motif]

cl29593
Location:49 → 291

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_063286095.1 → XP_063142165.1 intraflagellar transport protein 122 homolog isoform X6

UniProtKB/TrEMBL

A0A8I5ZMU0

Related

ENSRNOP00000014733.8, ENSRNOT00000014733.8
XM_039107643.2 → XP_038963571.1 intraflagellar transport protein 122 homolog isoform X8

UniProtKB/TrEMBL

A0A8J8XQ65

Conserved Domains (2) summary

sd00039
Location:15 → 51

7WD40; WD40 repeat [structural motif]

cl29593
Location:12 → 190

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 ...