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VEPH1 ventricular zone expressed PH domain containing 1 [ Homo sapiens (human) ]

Gene ID: 79674, updated on 10-Dec-2024

Summary

Official Symbol
VEPH1provided by HGNC
Official Full Name
ventricular zone expressed PH domain containing 1provided by HGNC
Primary source
HGNC:HGNC:25735
See related
Ensembl:ENSG00000197415 MIM:609594; AllianceGenome:HGNC:25735
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
MELT; VEPH
Summary
Predicted to enable phosphatidylinositol-5-phosphate binding activity. Involved in negative regulation of SMAD protein signal transduction and negative regulation of transforming growth factor beta receptor signaling pathway. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Biased expression in lung (RPKM 12.0), adrenal (RPKM 8.2) and 8 other tissues See more
Orthologs
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Genomic context

See VEPH1 in Genome Data Viewer
Location:
3q25.31-q25.32
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (157259742..157503605, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (160034311..160278175, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (156977531..157221394, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928236 Neighboring gene uncharacterized LOC105374179 Neighboring gene VISTA enhancer hs2571 Neighboring gene NANOG hESC enhancer GRCh37_chr3:156973526-156974057 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:156992312-156992853 Neighboring gene PCBP2 pseudogene 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:157216797-157217361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:157217362-157217925 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:157220998-157221232 Neighboring gene pentraxin 3 Neighboring gene CRISPRi-validated cis-regulatory element chr3.4666 Neighboring gene solute carrier family 66 member 1 like, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_65660 Neighboring gene VISTA enhancer hs638 Neighboring gene RN7SK pseudogene 46

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association study of smoking behaviours in patients with COPD.
EBI GWAS Catalog
Genome-wide meta-analysis for severe diabetic retinopathy.
EBI GWAS Catalog

Interactions

General gene information

Clone Names

  • FLJ12604, KIAA1692, MGC111426, MGC126709, MGC142115

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylinositol-5-phosphate binding  
enables protein binding PubMed 
Component Evidence Code Pubs
is_active_in plasma membrane  

General protein information

Preferred Names
ventricular zone-expressed PH domain-containing protein homolog 1
Names
protein melted
ventricular zone expressed PH domain homolog 1

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001167911.2NP_001161383.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AB051479, AC020630, AC092944, BC111017
    Consensus CDS
    CCDS54662.1
    UniProtKB/Swiss-Prot
    Q14D04
    Related
    ENSP00000376578.2, ENST00000392833.6
    Conserved Domains (2) summary
    cd01264
    Location:671779
    PH_MELT_VEPH1; Melted pleckstrin homology (PH) domain
    pfam00169
    Location:672774
    PH; PH domain
  2. NM_001167912.2NP_001161384.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform 1

    See identical proteins and their annotated locations for NP_001161384.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AB051479, AC020630, AC092944
    Consensus CDS
    CCDS3179.1
    UniProtKB/Swiss-Prot
    D3DNL0, F5GZ91, Q14D04, Q2TAA9, Q3MIX2, Q6PEL3, Q86TL5, Q8TCR3, Q96SP7, Q9C0H1, Q9H9Q7
    Related
    ENSP00000354919.2, ENST00000362010.7
    Conserved Domains (1) summary
    cd01264
    Location:716824
    PH_MELT_VEPH1; Melted pleckstrin homology (PH) domain
  3. NM_001167915.3NP_001161387.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform 3

    See identical proteins and their annotated locations for NP_001161387.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, 3' UTR, and coding region, compared to variant 1. Variants 4 and 5 encode the same isoform (3), which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC020630, BC057999, BC078142
    Consensus CDS
    CCDS54661.1
    UniProtKB/Swiss-Prot
    Q14D04
    Related
    ENSP00000419193.1, ENST00000494677.5
  4. NM_001167916.3NP_001161388.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform 3

    See identical proteins and their annotated locations for NP_001161388.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, 3' UTR, and coding region, compared to variant 1. Variants 4 and 5 encode the same isoform (3), which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC020630, BC057999
    Consensus CDS
    CCDS54661.1
    UniProtKB/Swiss-Prot
    Q14D04
    Related
    ENSP00000417268.1, ENST00000468233.5
  5. NM_001167917.1NP_001161389.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform 5

    See identical proteins and their annotated locations for NP_001161389.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, 3' UTR, and coding region, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC020630, BG194590, DA887051
    Consensus CDS
    CCDS54663.1
    UniProtKB/TrEMBL
    C9JRT0
    Related
    ENSP00000443868.1, ENST00000537559.5
  6. NM_024621.2NP_078897.2  ventricular zone-expressed PH domain-containing protein homolog 1 isoform 1

    See identical proteins and their annotated locations for NP_078897.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC020630, AC092944, AK027625
    Consensus CDS
    CCDS3179.1
    UniProtKB/Swiss-Prot
    D3DNL0, F5GZ91, Q14D04, Q2TAA9, Q3MIX2, Q6PEL3, Q86TL5, Q8TCR3, Q96SP7, Q9C0H1, Q9H9Q7
    Related
    ENSP00000376577.2, ENST00000392832.6
    Conserved Domains (1) summary
    cd01264
    Location:716824
    PH_MELT_VEPH1; Melted pleckstrin homology (PH) domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    157259742..157503605 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047448927.1XP_047304883.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  2. XM_047448922.1XP_047304878.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X3

  3. XM_024453748.2XP_024309516.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X2

    UniProtKB/Swiss-Prot
    D3DNL0, F5GZ91, Q14D04, Q2TAA9, Q3MIX2, Q6PEL3, Q86TL5, Q8TCR3, Q96SP7, Q9C0H1, Q9H9Q7
    Conserved Domains (1) summary
    cd01264
    Location:716824
    PH_MELT_VEPH1; Melted pleckstrin homology (PH) domain
  4. XM_024453747.2XP_024309515.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X2

    UniProtKB/Swiss-Prot
    D3DNL0, F5GZ91, Q14D04, Q2TAA9, Q3MIX2, Q6PEL3, Q86TL5, Q8TCR3, Q96SP7, Q9C0H1, Q9H9Q7
    Conserved Domains (1) summary
    cd01264
    Location:716824
    PH_MELT_VEPH1; Melted pleckstrin homology (PH) domain
  5. XM_047448921.1XP_047304877.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X3

  6. XM_024453746.2XP_024309514.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X2

    UniProtKB/Swiss-Prot
    D3DNL0, F5GZ91, Q14D04, Q2TAA9, Q3MIX2, Q6PEL3, Q86TL5, Q8TCR3, Q96SP7, Q9C0H1, Q9H9Q7
    Conserved Domains (1) summary
    cd01264
    Location:716824
    PH_MELT_VEPH1; Melted pleckstrin homology (PH) domain
  7. XM_047448923.1XP_047304879.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  8. XM_047448924.1XP_047304880.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  9. XM_011513135.3XP_011511437.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X4

    Conserved Domains (2) summary
    cd01264
    Location:671779
    PH_MELT_VEPH1; Melted pleckstrin homology (PH) domain
    pfam00169
    Location:672774
    PH; PH domain
  10. XM_011513134.3XP_011511436.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X1

    Conserved Domains (2) summary
    cd01264
    Location:727835
    PH_MELT_VEPH1; Melted pleckstrin homology (PH) domain
    pfam00169
    Location:728830
    PH; PH domain
  11. XM_047448925.1XP_047304881.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  12. XM_047448926.1XP_047304882.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  13. XM_047448928.1XP_047304884.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X6

  14. XM_047448929.1XP_047304885.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X7

  15. XM_047448930.1XP_047304886.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X7

  16. XM_024453750.2XP_024309518.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X8

    UniProtKB/TrEMBL
    C9JRT0
  17. XM_024453749.2XP_024309517.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X8

    UniProtKB/TrEMBL
    C9JRT0
  18. XM_047448931.1XP_047304887.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X8

    UniProtKB/TrEMBL
    C9JRT0

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    160034311..160278175 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347875.1XP_054203850.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  2. XM_054347870.1XP_054203845.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X3

  3. XM_054347866.1XP_054203841.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X2

    UniProtKB/Swiss-Prot
    D3DNL0, F5GZ91, Q14D04, Q2TAA9, Q3MIX2, Q6PEL3, Q86TL5, Q8TCR3, Q96SP7, Q9C0H1, Q9H9Q7
  4. XM_054347867.1XP_054203842.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X2

    UniProtKB/Swiss-Prot
    D3DNL0, F5GZ91, Q14D04, Q2TAA9, Q3MIX2, Q6PEL3, Q86TL5, Q8TCR3, Q96SP7, Q9C0H1, Q9H9Q7
  5. XM_054347868.1XP_054203843.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X3

  6. XM_054347865.1XP_054203840.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X2

    UniProtKB/Swiss-Prot
    D3DNL0, F5GZ91, Q14D04, Q2TAA9, Q3MIX2, Q6PEL3, Q86TL5, Q8TCR3, Q96SP7, Q9C0H1, Q9H9Q7
  7. XM_054347871.1XP_054203846.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  8. XM_054347872.1XP_054203847.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  9. XM_054347869.1XP_054203844.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X4

  10. XM_054347864.1XP_054203839.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X1

  11. XM_054347873.1XP_054203848.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  12. XM_054347874.1XP_054203849.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X5

  13. XM_054347876.1XP_054203851.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X6

  14. XM_054347877.1XP_054203852.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X7

  15. XM_054347878.1XP_054203853.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X7

  16. XM_054347881.1XP_054203856.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X8

    UniProtKB/TrEMBL
    C9JRT0
  17. XM_054347879.1XP_054203854.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X8

    UniProtKB/TrEMBL
    C9JRT0
  18. XM_054347880.1XP_054203855.1  ventricular zone-expressed PH domain-containing protein homolog 1 isoform X8

    UniProtKB/TrEMBL
    C9JRT0
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