RAB5IF (RAB5 interacting factor) - Rat Genome Database

Name: RAB5IF
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: RAB5IF (RAB5 interacting factor) Sus scrofa

Analyze

Symbol:

RAB5IF

Name:

RAB5 interacting factor

RGD ID:

14236573

Description:

INVOLVED IN mitochondrial respirasome assembly (inferred); multi-pass transmembrane protein insertion into ER membrane (inferred); ASSOCIATED WITH craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2 (ortholog); craniofacial dysmorphism, skeletal anomalies, and mental retardation syndrome (ortholog); focal epilepsy (ortholog); FOUND IN endoplasmic reticulum membrane (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

C17H20orf24; chromosome 17 C20orf24 homolog; RAB5-interacting protein; uncharacterized protein C20orf24 homolog

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	RAB5IF (RAB5 interacting factor)	HGNC	NCBI, Panther
Mus musculus (house mouse):	Rab5if (RAB5 interacting factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Rab5if (RAB5 interacting factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Rab5if (RAB5 interacting factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RAB5IF (RAB5 interacting factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RAB5IF (RAB5 interacting factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rab5if (RAB5 interacting factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	RAB5IF (RAB5 interacting factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rab5if (RAB5 interacting factor)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	39,868,882 - 39,882,690 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	17	39,868,849 - 39,878,623 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2 (ISO)

craniofacial dysmorphism, skeletal anomalies, and mental retardation syndrome (ISO)

focal epilepsy (ISO)

Hypertelorism (ISO)

intellectual disability (ISO)

Macrocephaly (ISO)

Micrognathism (ISO)

scoliosis (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

mitochondrial respirasome assembly (IEA)

multi-pass transmembrane protein insertion into ER membrane (IEA)

Cellular Component

endoplasmic reticulum (IEA)

endoplasmic reticulum membrane (IEA,ISO)

membrane (IEA)

mitochondrial respirasome (IEA)

multi-pass translocon complex (IEA)

Molecular Function

protein binding (ISO)

References

Additional References at PubMed

PMID:14681463	PMID:15679890	PMID:17145712	PMID:30032202

Genomics

Comparative Map Data

RAB5IF
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	39,868,882 - 39,882,690 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	17	39,868,849 - 39,878,623 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

RAB5IF
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	20	36,605,779 - 36,612,557 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	20	36,605,779 - 36,612,557 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	20	35,234,182 - 35,240,960 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	20	34,667,581 - 34,674,374 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	20	34,667,580 - 34,674,372	NCBI
Celera	20	31,941,205 - 31,948,034 (+)	NCBI		Celera
Cytogenetic Map	20	q11.23	NCBI
HuRef	20	31,970,191 - 31,977,007 (+)	NCBI		HuRef
CHM1_1	20	35,135,842 - 35,142,665 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	20	38,329,630 - 38,336,422 (+)	NCBI		T2T-CHM13v2.0

Rab5if
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	156,705,042 - 156,715,483 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	156,705,048 - 156,715,483 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	156,863,122 - 156,873,563 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	156,863,128 - 156,873,563 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	156,688,858 - 156,699,299 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	156,554,569 - 156,565,000 (+)	NCBI		MGSCv36	mm8
Celera	2	162,798,901 - 162,809,285 (+)	NCBI		Celera
Cytogenetic Map	2	H1	NCBI
cM Map	2	77.89	NCBI

Rab5if
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	165,818,060 - 165,828,071 (+)	NCBI		GRCr8
mRatBN7.2	3	145,357,990 - 145,368,012 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	145,357,861 - 145,368,012 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	149,223,457 - 149,233,468 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	157,840,175 - 157,850,186 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	155,579,229 - 155,589,245 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	152,933,771 - 152,943,780 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	152,933,771 - 152,943,777 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	158,753,364 - 158,763,373 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	147,266,788 - 147,276,798 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	147,172,696 - 147,182,704 (+)	NCBI
Celera	3	144,074,935 - 144,085,079 (+)	NCBI		Celera
Cytogenetic Map	3	q42	NCBI

Rab5if
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955422	25,003,195 - 25,017,380 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955422	25,003,195 - 25,017,380 (-)	NCBI	ChiLan1.0	ChiLan1.0

RAB5IF
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	21	42,343,944 - 42,350,756 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	20	42,337,106 - 42,343,694 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	20	32,938,953 - 32,945,648 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	20	34,059,109 - 34,065,624 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	20	34,059,109 - 34,065,624 (+)	Ensembl	panpan1.1		panPan2

RAB5IF
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	24	25,386,406 - 25,396,045 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	24	25,386,420 - 25,395,713 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	24	25,032,319 - 25,041,948 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	24	26,083,966 - 26,093,618 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	24	26,083,960 - 26,093,618 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	24	25,362,586 - 25,372,419 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	24	25,461,426 - 25,471,315 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	24	25,952,224 - 25,961,852 (+)	NCBI		UU_Cfam_GSD_1.0

Rab5if
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	174,309,729 - 174,320,977 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936561	4,428,231 - 4,439,897 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936561	4,428,499 - 4,439,786 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RAB5IF
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	2	57,473,593 - 57,477,322 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	2	57,473,596 - 57,477,700 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023669489	1,625 - 3,948 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Rab5if
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624842	2,882,097 - 2,894,973 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624842	2,882,252 - 2,895,047 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in RAB5IF
122 total Variants

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	hemolymphoid system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system
High
Medium	9	4	3	5	2	18	2	2	3
Low	1					5		1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_021077901	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000106	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK350513	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY610269	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY803086	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CU607085	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GFLN01049964	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSSCT00000037352 ⟹ ENSSSCP00000039753

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1 Ensembl	17	39,868,892 - 39,878,619 (+)	Ensembl

RefSeq Acc Id:

ENSSSCT00000042521 ⟹ ENSSSCP00000048163

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1 Ensembl	17	39,868,882 - 39,882,690 (+)	Ensembl

RefSeq Acc Id:

XM_021077901 ⟹ XP_020933560

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	17	39,868,849 - 39,878,623 (+)	NCBI

Sequence:

show sequence

GCGGTGCTGCGTTGCTCCGCCCACCGACCTCCTGGTCTCGGCCGAGAGAGCAGAGCCGGGCTGC
CTGGTTAGGTGCGGGCAGCCGCAGGCGCGCCGCCGAACACGTCCGCTGAGTGCCACCACCACCG
CCCGGCGCCCCGTGACCCGTGACTCCAGACCCCGACCCCTTTTAGATCGGCCCGCGCGCCCCAG
GCCCGGCCCGGGCGGCGCGACGGGAGGATGAGCGGCGGGCGGCGGAAGGAGGAGCCGCCTCAGC
CGCAGCTGGCCAACGGGGCCCTCAAAGTCTCTGTCTGGAGCAAAGTGCTGCGGAGCGACGCGGC
CTGGGAGGACAAGGATGAATTTTTAGATGTGATCTACTGGTTCCGACAGATCATTGCTGTGGTC
CTAGGTGTCATTTGGGGAGTGCTACCCTTGCGAGGTTTCTTGGGAATAGCAGGATTCTGCCTGA
TCAATGCAGGTGTCCTGTACCTCTACTTCAGCAACTACCTACAGATAGATGAGGAAGAATATGG
TGGCACATGGGAGCTCACGAAAGAAGGGTTTATGACGTCATTTGCCTTGTTCATGGTCATTTGG
ATCATCTTTTACACTGCCATCCACTATGACTGACGGTACAGCCCCCACCTGCTCCCTGTCTGGT
CCGAAAGACCCTCTTAGTTACAGCACAGAAACATGATTGTTAGGGGCACCCCAGCCATGTGGAA
CCTGGAAGACTCATGTTTCCTGGACTGAGAAATCAGTGTTGGGCGTCAGTGTTTTCTGCAGGGG
TTGTGACCTGAAACTTTTTAAAGAAACATCCACCTTTTGGAGAAGCATTTCTGAATTGTCCATC
ACCAACCGTTTCTTCTTGGATACCATCATGAAACACCTATTTGCCGATTGGAGCTGTCCTTTAA
TTTGATGCATCTCTGGATCTGGATGAAACATTAAATTGTCTTTCTTCTCCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_020933560	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSSCP00000039753.2
	ENSSSCP00000048163
	ENSSSCP00000048163.2
	ENSSSCP00015005410.1
	ENSSSCP00025014758.1
	ENSSSCP00030012992.1
	ENSSSCP00035013867.1
	ENSSSCP00040028612.1
	ENSSSCP00045009508.1
	ENSSSCP00050035823.1
	ENSSSCP00055027825.1
	ENSSSCP00060046151.1
	ENSSSCP00065039671.1
	ENSSSCP00070014103.1

RefSeq Acc Id:	XP_020933560 ⟸ XM_021077901
- UniProtKB:	A0A4X1TEK9 (UniProtKB/TrEMBL), A0A287AW52 (UniProtKB/TrEMBL), A0A8D0ZAE0 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSGGRRKEEPPQPQLANGALKVSVWSKVLRSDAAWEDKDEFLDVIYWFRQIIAVVLGVIWGVLP LRGFLGIAGFCLINAGVLYLYFSNYLQIDEEEYGGTWELTKEGFMTSFALFMVIWIIFYTAIHY D hide sequence

RefSeq Acc Id:

ENSSSCP00000048163 ⟸ ENSSSCT00000042521

RefSeq Acc Id:

ENSSSCP00000039753 ⟸ ENSSSCT00000037352

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00000039201	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCG00015010643	UniProtKB/TrEMBL
	ENSSSCG00025026171	UniProtKB/TrEMBL
	ENSSSCG00030020972	UniProtKB/TrEMBL
	ENSSSCG00035026515	UniProtKB/TrEMBL
	ENSSSCG00040049927	UniProtKB/TrEMBL
	ENSSSCG00045008190	UniProtKB/TrEMBL
	ENSSSCG00050061206	UniProtKB/TrEMBL
	ENSSSCG00055017894	UniProtKB/TrEMBL
	ENSSSCG00060076626	UniProtKB/TrEMBL
	ENSSSCG00065066068	UniProtKB/TrEMBL
	ENSSSCG00070008790	UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00000037352.2	UniProtKB/TrEMBL
	ENSSSCT00000042521	ENTREZGENE
	ENSSSCT00000042521.2	UniProtKB/TrEMBL
	ENSSSCT00015013945.1	UniProtKB/TrEMBL
	ENSSSCT00025035368.1	UniProtKB/TrEMBL
	ENSSSCT00030029017.1	UniProtKB/TrEMBL
	ENSSSCT00035034983.1	UniProtKB/TrEMBL
	ENSSSCT00040067353.1	UniProtKB/TrEMBL
	ENSSSCT00045013748.1	UniProtKB/TrEMBL
	ENSSSCT00050083412.1	UniProtKB/TrEMBL
	ENSSSCT00055035042.1	UniProtKB/TrEMBL
	ENSSSCT00060105146.1	UniProtKB/TrEMBL
	ENSSSCT00065090667.1	UniProtKB/TrEMBL
	ENSSSCT00070017039.1	UniProtKB/TrEMBL
InterPro	Rab5ip	UniProtKB/TrEMBL
	Rab5IP_fam	UniProtKB/TrEMBL
NCBI Gene	RAB5IF	ENTREZGENE
PANTHER	PTHR12906	UniProtKB/TrEMBL
	RESPIRASOME COMPLEX ASSEMBLY FACTOR 1	UniProtKB/TrEMBL
Pfam	Rab5ip	UniProtKB/TrEMBL
UniProt	A0A287A7K9_PIG	UniProtKB/TrEMBL
	A0A287AW52	ENTREZGENE, UniProtKB/TrEMBL
	A0A4X1TEK9	ENTREZGENE, UniProtKB/TrEMBL
	A0A8D0ZAE0	ENTREZGENE, UniProtKB/TrEMBL
VGNC ID	VGNC:98271	ENTREZGENE

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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