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YIPF2 Yip1 domain family member 2 [ Homo sapiens (human) ]

Gene ID: 78992, updated on 5-Mar-2024

Summary

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Official Symbol
YIPF2provided by HGNC
Official Full Name
Yip1 domain family member 2provided by HGNC
Primary source
HGNC:HGNC:28476
See related
Ensembl:ENSG00000130733 MIM:617522; AllianceGenome:HGNC:28476
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Yip5C; FinGER2; YIPFbeta3B
Summary
Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Located in Golgi apparatus subcompartment and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 22.9), placenta (RPKM 21.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19p13.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (10922193..10928639, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (11049196..11055650, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (11032869..11039315, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10945386-10946023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10946661-10947297 Neighboring gene chromosome 19 open reading frame 38 Neighboring gene HIKESHI pseudogene 2 Neighboring gene transmembrane p24 trafficking protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10973529-10974377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13997 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10984976-10985476 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10985477-10985977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13999 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10989664-10990506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10991348-10992190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10992191-10993032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10993033-10993874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10993875-10994715 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11004683-11005484 Neighboring gene coactivator associated arginine methyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11009921-11010538 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:11015702-11015889 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:11031708-11031887 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11037946-11038648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11038649-11039349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10095 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:11046750-11047081 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:11048011-11048510 Neighboring gene translocase of inner mitochondrial membrane 29 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14001 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11087822-11088514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11120526-11121026 Neighboring gene RNA, 7SL, cytoplasmic 192, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. YIPF2 promotes chemotherapeutic agent-mediated apoptosis via enhancing TNFRSF10B recycling to plasma membrane in non-small cell lung cancer cells. Wang Y, et al. Cell Death Dis, 2020 Apr 17. PMID 32303681, Free PMC Article
  2. YIPF2 is a novel Rab-GDF that enhances HCC malignant phenotypes by facilitating CD147 endocytic recycle. Qi S, et al. Cell Death Dis, 2019 Jun 12. PMID 31189879, Free PMC Article
  3. YIPF1, YIPF2, and YIPF6 are medial-/trans-Golgi and trans-Golgi network-localized Yip domain family proteins, which play a role in the Golgi reassembly and glycan synthesis. Soonthornsit J, et al. Exp Cell Res, 2017 Apr 15. PMID 28286305
  4. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article
  5. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. YIPF2 promotes chemotherapeutic agent-mediated apoptosis via enhancing TNFRSF10B recycling to plasma membrane in non-small cell lung cancer cells.
    Title: YIPF2 promotes chemotherapeutic agent-mediated apoptosis via enhancing TNFRSF10B recycling to plasma membrane in non-small cell lung cancer cells.
  2. YIPF2 is a new trafficking determinant essential for CD147 glycosylation and transport. YIPF2-controlled ER-Golgi trafficking signature promotes CD147-medated malignant phenotypes in hepatocellular carcinoma.
    Title: YIPF2 is a novel Rab-GDF that enhances HCC malignant phenotypes by facilitating CD147 endocytic recycle.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC3262

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi medial cisterna IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi trans cisterna IDA
Inferred from Direct Assay
more info
 PubMed 
located_in late endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 
located_in transport vesicle IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
protein YIPF2
Names
YIP1 family member 2

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)

  1. NM_001321439.2 → NP_001308368.1  protein YIPF2 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC011442, BC000056, HY020827
    Consensus CDS
    CCDS12251.1
    UniProtKB/Swiss-Prot
    Q9BWQ6
    Related
    ENSP00000466055.1, ENST00000586748.6
    Conserved Domains (1) summary
    pfam04893
    Location:87 → 248
    Yip1; Yip1 domain

  2. NM_001321440.2 → NP_001308369.1  protein YIPF2 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC011442, BE275116, BM554546
    Consensus CDS
    CCDS82293.1
    UniProtKB/TrEMBL
    K7ENM8
    Related
    ENSP00000467019.1, ENST00000590329.5
    Conserved Domains (1) summary
    pfam04893
    Location:122 → 209
    Yip1; Yip1 domain

  3. NM_024029.5 → NP_076934.1  protein YIPF2 isoform 1

    See identical proteins and their annotated locations for NP_076934.1

    Status: VALIDATED

    Source sequence(s)
    AC011442, BC013014, BX327495
    Consensus CDS
    CCDS12251.1
    UniProtKB/Swiss-Prot
    Q9BWQ6
    Related
    ENSP00000253031.1, ENST00000253031.6
    Conserved Domains (1) summary
    pfam04893
    Location:87 → 248
    Yip1; Yip1 domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    10922193..10928639 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439386.1 → XP_047295342.1  protein YIPF2 isoform X2

  2. XM_047439387.1 → XP_047295343.1  protein YIPF2 isoform X2

  3. XM_024451699.2 → XP_024307467.1  protein YIPF2 isoform X1

    UniProtKB/Swiss-Prot
    Q9BWQ6
    Conserved Domains (1) summary
    pfam04893
    Location:87 → 248
    Yip1; Yip1 domain

  4. XM_011528271.3 → XP_011526573.1  protein YIPF2 isoform X2

    Conserved Domains (1) summary
    pfam04893
    Location:81 → 219
    Yip1; Yip1 domain

  5. XM_024451700.2 → XP_024307468.1  protein YIPF2 isoform X2

    Conserved Domains (1) summary
    pfam04893
    Location:81 → 219
    Yip1; Yip1 domain

  6. XM_011528270.3 → XP_011526572.1  protein YIPF2 isoform X1

    See identical proteins and their annotated locations for XP_011526572.1

    UniProtKB/Swiss-Prot
    Q9BWQ6
    Conserved Domains (1) summary
    pfam04893
    Location:87 → 248
    Yip1; Yip1 domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    11049196..11055650 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322058.1 → XP_054178033.1  protein YIPF2 isoform X2

  2. XM_054322054.1 → XP_054178029.1  protein YIPF2 isoform X1

    UniProtKB/Swiss-Prot
    Q9BWQ6

  3. XM_054322057.1 → XP_054178032.1  protein YIPF2 isoform X2

  4. XM_054322053.1 → XP_054178028.1  protein YIPF2 isoform X1

    UniProtKB/Swiss-Prot
    Q9BWQ6

  5. XM_054322056.1 → XP_054178031.1  protein YIPF2 isoform X2

  6. XM_054322055.1 → XP_054178030.1  protein YIPF2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BWQ6.1 GenPept UniProtKB/Swiss-Prot:Q9BWQ6

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