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ZFYVE28 zinc finger FYVE-type containing 28 [ Homo sapiens (human) ]

Gene ID: 57732, updated on 17-Jun-2019

Summary

Official Symbol
ZFYVE28provided by HGNC
Official Full Name
zinc finger FYVE-type containing 28provided by HGNC
Primary source
HGNC:HGNC:29334
See related
Ensembl:ENSG00000159733 MIM:614176
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
LST2; LYST2
Expression
Ubiquitous expression in testis (RPKM 1.1), brain (RPKM 1.1) and 25 other tissues See more
Orthologs

Genomic context

See ZFYVE28 in Genome Data Viewer
Location:
4p16.3
Exon count:
23
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (2269585..2418698, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (2271324..2420370, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene DNA polymerase nu Neighboring gene cytochrome c oxidase subunit 6B1 pseudogene 5 Neighboring gene HAUS augmin like complex subunit 3 Neighboring gene microRNA 4800 Neighboring gene MAX dimerization protein 4 Neighboring gene Spi-C transcription factor (Spi-1/PU.1 related) pseudogene Neighboring gene RNA, 7SL, cytoplasmic 589, pseudogene Neighboring gene uncharacterized LOC105374352 Neighboring gene uncharacterized LOC107986249 Neighboring gene cilia and flagella associated protein 99 Neighboring gene uncharacterized LOC105374353 Neighboring gene uncharacterized LOC107986250

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
NHGRI GWA Catalog
Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC43699, MGC61592

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
early endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lateral signaling target protein 2 homolog
Names
hLst2
zinc finger FYVE domain-containing protein 28
zinc finger, FYVE domain containing 28

NCBI Reference Sequences (RefSeq)

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_001172656.2NP_001166127.1  lateral signaling target protein 2 homolog isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and lacks an alternate in-frame exon, compared to variant 1. The resulting isoform (3) has a longer N-terminus and lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AB046863, AK293775, AK294710, AL645924, BC032605, BC137309, BM128958
    Consensus CDS
    CCDS54711.1
    UniProtKB/Swiss-Prot
    Q9HCC9
    Related
    ENSP00000425706.1, ENST00000511071.5
    Conserved Domains (1) summary
    cd15731
    Location:780844
    FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins
  2. NM_001172657.2NP_001166128.1  lateral signaling target protein 2 homolog isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (4) has a longer N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL158068, AL645924, BC032605, BC053664
    Consensus CDS
    CCDS54712.1
    UniProtKB/Swiss-Prot
    Q9HCC9
    Related
    ENSP00000423694.1, ENST00000503000.1
  3. NM_001172658.2NP_001166129.1  lateral signaling target protein 2 homolog isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (5) has a longer N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL158068, AL645924, BC032605, BC035793, BC137310
    Consensus CDS
    CCDS54710.1
    UniProtKB/Swiss-Prot
    Q9HCC9
    Related
    ENSP00000422638.1, ENST00000509171.5
  4. NM_001172659.2NP_001166130.1  lateral signaling target protein 2 homolog isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
    Source sequence(s)
    AB046863, AK294874, AK316484, BC035793, BC137310, BM128958
    Consensus CDS
    CCDS54708.1
    UniProtKB/Swiss-Prot
    Q9HCC9
    Related
    ENSP00000426299.1, ENST00000515312.5
    Conserved Domains (1) summary
    cd15731
    Location:740804
    FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins
  5. NM_001172660.2NP_001166131.1  lateral signaling target protein 2 homolog isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (6) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK316484, AL158068, BC035793, BC137310
    Consensus CDS
    CCDS54709.1
    UniProtKB/Swiss-Prot
    Q9HCC9
    Related
    ENSP00000425766.1, ENST00000515169.5
  6. NM_020972.3NP_066023.2  lateral signaling target protein 2 homolog isoform 2

    See identical proteins and their annotated locations for NP_066023.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses an upstream start codon, compared to variant 1. The resulting isoform (2) has a longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AB046863, AK294874, AL645924, BC032605, BC137310, BM128958
    Consensus CDS
    CCDS33942.1
    UniProtKB/Swiss-Prot
    Q9HCC9
    Related
    ENSP00000290974.2, ENST00000290974.6
    Conserved Domains (1) summary
    cd15731
    Location:810874
    FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    2269585..2418698 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713902.3XP_006713965.1  lateral signaling target protein 2 homolog isoform X4

  2. XM_017008503.1XP_016863992.1  lateral signaling target protein 2 homolog isoform X3

  3. XM_006713900.3XP_006713963.1  lateral signaling target protein 2 homolog isoform X1

    Conserved Domains (1) summary
    cl22851
    Location:810845
    PHD_SF; PHD finger superfamily
  4. XM_017008504.2XP_016863993.1  lateral signaling target protein 2 homolog isoform X5

  5. XM_017008502.1XP_016863991.1  lateral signaling target protein 2 homolog isoform X2

  6. XM_017008505.1XP_016863994.1  lateral signaling target protein 2 homolog isoform X7

    UniProtKB/Swiss-Prot
    Q9HCC9
  7. XM_011513540.2XP_011511842.1  lateral signaling target protein 2 homolog isoform X6

    Conserved Domains (1) summary
    cl22851
    Location:696731
    PHD_SF; PHD finger superfamily
  8. XM_017008510.2XP_016863999.1  lateral signaling target protein 2 homolog isoform X13

  9. XM_011513541.3XP_011511843.1  lateral signaling target protein 2 homolog isoform X9

  10. XM_017008506.1XP_016863995.1  lateral signaling target protein 2 homolog isoform X8

  11. XM_017008509.1XP_016863998.1  lateral signaling target protein 2 homolog isoform X12

  12. XM_017008508.1XP_016863997.1  lateral signaling target protein 2 homolog isoform X11

  13. XM_017008507.1XP_016863996.1  lateral signaling target protein 2 homolog isoform X10

  14. XM_006713904.3XP_006713967.1  lateral signaling target protein 2 homolog isoform X14

    See identical proteins and their annotated locations for XP_006713967.1

RNA

  1. XR_001741314.1 RNA Sequence

  2. XR_001741313.1 RNA Sequence

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