Ift140 intraflagellar transport 140 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ift140provided by MGI
Official Full Name: intraflagellar transport 140provided by MGI
Primary source: MGI:MGI:2146906
See related: Ensembl:ENSMUSG00000024169 AllianceGenome:MGI:2146906
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Tce5; Wdtc2; mKIAA0590
Summary: Acts upstream of or within several processes, including cilium organization; embryonic organ development; and nervous system development. Located in cytoskeleton and photoreceptor cell cilium. Part of intraciliary transport particle A. Is expressed in diaphragm; lung; metanephros; and retina. Used to study asphyxiating thoracic dystrophy 1 and short-rib thoracic dysplasia 9 with or without polydactyly. Human ortholog(s) of this gene implicated in retinitis pigmentosa and short-rib thoracic dysplasia 9 with or without polydactyly. Orthologous to human IFT140 (intraflagellar transport 140). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in testis adult (RPKM 39.8), liver E14.5 (RPKM 18.4) and 23 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 17 A3.3; 17 12.53 cM

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (25235056..25318461)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (25016083..25099499)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The role of IFT140 in early bone healing of tooth extraction sockets.
Title: The role of IFT140 in early bone healing of tooth extraction sockets.
Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E.
Title: Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E.
Lineage tracing of cells expressing the ciliary gene IFT140 during bone development.
Title: Lineage tracing of cells expressing the ciliary gene IFT140 during bone development.
results showed that, compared with many soft tissues,intraflagellar transport 140 (mRNA level) was highly expressed in bone
Title: Expression of IFT140 During Bone Development.
In a mouse model, results suggest that cilia gene IFT140 is essential in promoting dentin formation and reparation.
Title: Essential Role of IFT140 in Promoting Dentinogenesis.
findings demonstrate that IFT140 is a key regulator for male fertility and normal spermiogenesis in mice. It not only plays a role in sperm flagella assembling, but is also involved in critical assembly of proteins that interface between the germ cell plasma and the Sertoli cell.
Title: Intraflagellar transporter protein 140 (IFT140), a component of IFT-A complex, is essential for male fertility and spermiogenesis in mice.
This work is a strong support of a model of opsin transport where, once at the base of the cilium, the opsin is carried through the connecting cilium by an IFT complex that includes IFT140
Title: Distinct functions for IFT140 and IFT20 in opsin transport.
We have identified a novel ENU mutant allele of Ift140, which causes a mid-gestation embryonic lethal phenotype in homozygous mutant mice.We also report the identification of a homozygous recessive mutation in IFT140 in a Jeune syndrome patient.
Title: Cauli: a mouse strain with an Ift140 mutation that results in a skeletal ciliopathy modelling Jeune syndrome.

Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (5) 1 citation
Chemically induced (ENU) (2) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

AI661311 (e-PCR)
- UniSTS:166036

D17Jcs41 (e-PCR), detects polymorphism
- UniSTS:259282

D17Jcs42 (e-PCR), detects polymorphism
- UniSTS:259283

D13S289 (e-PCR), detects polymorphism
- UniSTS:39143

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell projection organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in cilium assembly	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic digit morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intraciliary retrograde transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intraciliary retrograde transport	IC Inferred by Curator more info	PubMed
acts_upstream_of_or_within intraciliary retrograde transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intraciliary retrograde transport	ISO Inferred from Sequence Orthology more info
involved_in intraciliary retrograde transport	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within intraciliary transport	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within limb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural tube patterning	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within non-motile cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within photoreceptor cell outer segment organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein localization to cilium	ISO Inferred from Sequence Orthology more info
involved_in regulation of cilium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of smoothened signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
located_in axoneme	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in centriole	IDA Inferred from Direct Assay more info	PubMed
located_in centrosome	ISO Inferred from Sequence Orthology more info
is_active_in ciliary basal body	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cilium	NAS Non-traceable Author Statement more info	PubMed
located_in cone photoreceptor outer segment	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	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	IDA Inferred from Direct Assay more info	PubMed
part_of intraciliary transport particle A	ISO Inferred from Sequence Orthology more info
located_in non-motile cilium	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor connecting cilium	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: intraflagellar transport protein 140 homolog

Names: T-complex expressed gene 5; WD and tetratricopeptide repeats 2; WD and tetratricopeptide repeats protein 2; intraflagellar transport 140 homolog

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001410317.1 → NP_001397246.1 intraflagellar transport protein 140 homolog isoform 2

Status: VALIDATED

Source sequence(s)

AC130711, AC154229
NM_001410318.1 → NP_001397247.1 intraflagellar transport protein 140 homolog isoform 2

Status: VALIDATED

Source sequence(s)

AC130711, AC154229
NM_001410319.1 → NP_001397248.1 intraflagellar transport protein 140 homolog isoform 1

Status: VALIDATED

Source sequence(s)

AC130711, AC154229

UniProtKB/Swiss-Prot

B2RSU5, E9PY46, Q2XQY6
NM_001410320.1 → NP_001397249.1 intraflagellar transport protein 140 homolog isoform 3

Status: VALIDATED

Source sequence(s)

AC130711, AC154229
NM_001410321.1 → NP_001397250.1 intraflagellar transport protein 140 homolog isoform 4

Status: VALIDATED

Source sequence(s)

AC130711, AC154229
NM_134126.4 → NP_598887.3 intraflagellar transport protein 140 homolog isoform 1

See identical proteins and their annotated locations for NP_598887.3

Status: VALIDATED

Source sequence(s)

AC130711, AC154229

Consensus CDS

CCDS28505.1

UniProtKB/Swiss-Prot

B2RSU5, E9PY46, Q2XQY6

UniProtKB/TrEMBL

A0A3B2W3F6

Related

ENSMUSP00000024983.6, ENSMUST00000024983.12

Conserved Domains (4) summary

COG0457
Location:832 → 1092

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

COG2319
Location:86 → 437

WD40; WD40 repeat [General function prediction only]

sd00039
Location:19 → 57

7WD40; WD40 repeat [structural motif]

pfam04097
Location:1047 → 1228

Nic96; Nup93/Nic96

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000083.7 Reference GRCm39 C57BL/6J

Range

25235056..25318461

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006523403.5 → XP_006523466.1 intraflagellar transport protein 140 homolog isoform X1

See identical proteins and their annotated locations for XP_006523466.1

UniProtKB/Swiss-Prot

B2RSU5, E9PY46, Q2XQY6

UniProtKB/TrEMBL

A0A3B2W3F6

Conserved Domains (4) summary

COG0457
Location:832 → 1092

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

COG2319
Location:86 → 437

WD40; WD40 repeat [General function prediction only]

sd00039
Location:19 → 57

7WD40; WD40 repeat [structural motif]

pfam04097
Location:1047 → 1228

Nic96; Nup93/Nic96
XM_006523404.4 → XP_006523467.1 intraflagellar transport protein 140 homolog isoform X2

UniProtKB/TrEMBL

A0A3B2W3F6

Related

ENSMUSP00000116163.2, ENSMUST00000137386.8

Conserved Domains (4) summary

COG0457
Location:832 → 1092

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

COG2319
Location:86 → 437

WD40; WD40 repeat [General function prediction only]

sd00039
Location:19 → 57

7WD40; WD40 repeat [structural motif]

pfam04097
Location:1047 → 1228

Nic96; Nup93/Nic96
XM_006523408.5 → XP_006523471.1 intraflagellar transport protein 140 homolog isoform X5

Conserved Domains (3) summary

COG2319
Location:86 → 437

WD40; WD40 repeat [General function prediction only]

sd00039
Location:19 → 57

7WD40; WD40 repeat [structural motif]

pfam12928
Location:455 → 506

tRNA_int_end_N2; tRNA-splicing endonuclease subunit sen54 N-term
XM_006523407.5 → XP_006523470.1 intraflagellar transport protein 140 homolog isoform X4

Conserved Domains (2) summary

COG2319
Location:86 → 437

WD40; WD40 repeat [General function prediction only]

sd00039
Location:19 → 57

7WD40; WD40 repeat [structural motif]