U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    NPNT nephronectin [ Homo sapiens (human) ]

    Gene ID: 255743, updated on 9-Dec-2024

    Summary

    Official Symbol
    NPNTprovided by HGNC
    Official Full Name
    nephronectinprovided by HGNC
    Primary source
    HGNC:HGNC:27405
    See related
    Ensembl:ENSG00000168743 MIM:610306; AllianceGenome:HGNC:27405
    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
    POEM; EGFL6L
    Summary
    Predicted to enable integrin binding activity. Predicted to be involved in several processes, including cell-cell adhesion mediated by integrin; positive regulation of ERK1 and ERK2 cascade; and positive regulation of osteoblast differentiation. Predicted to act upstream of or within positive regulation of transforming growth factor beta receptor signaling pathway. Located in collagen-containing extracellular matrix and extracellular exosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in thyroid (RPKM 91.1), lung (RPKM 60.2) and 10 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NPNT in Genome Data Viewer
    Location:
    4q24
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (105895471..105971671)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (109206597..109282798)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (106816628..106892828)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene glutathione S-transferase C-terminal domain containing Neighboring gene uncharacterized LOC124900749 Neighboring gene GSTCD antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15611 Neighboring gene Sharpr-MPRA regulatory region 231 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:106919539-106920322 Neighboring gene uncharacterized LOC101929577 Neighboring gene Sharpr-MPRA regulatory region 11278 Neighboring gene TBC1 domain containing kinase Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:107041415-107042014 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:107134215-107134877 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:107134878-107135539 Neighboring gene NANOG hESC enhancer GRCh37_chr4:107194925-107195427 Neighboring gene uncharacterized LOC124900750

    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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog
    Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables integrin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables integrin binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in branching involved in ureteric bud morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in cell-cell adhesion mediated by integrin ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in cell-matrix adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in cellular response to tumor necrosis factor ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in establishment of protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in extracellular matrix organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in pilomotor reflex IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of ERK1 and ERK2 cascade ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of cell-substrate adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of smooth muscle contraction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transforming growth factor beta receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smooth muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transforming growth factor beta receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ureteric bud development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in basement membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in collagen-containing extracellular matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in smooth muscle contractile fiber IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    nephronectin
    Names
    preosteoblast EGF-like repeat protein with MAM domain

    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_001033047.3NP_001028219.1  nephronectin isoform B precursor

      See identical proteins and their annotated locations for NP_001028219.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1, and encodes a shorter protein (isoform B), compared to isoform A. This variant is also known as isoform 1.
      Source sequence(s)
      AC109361, AK290029, AK295772, AW607534
      Consensus CDS
      CCDS34046.1
      UniProtKB/Swiss-Prot
      A6NFT9, A8K1W4, B4DIT4, B4DYK3, B4E2H7, B4E3H2, D6RCA1, E9PCK8, E9PCQ1, E9PE64, E9PF04, Q6UXI9
      UniProtKB/TrEMBL
      D6RH31
      Related
      ENSP00000369323.2, ENST00000379987.7
      Conserved Domains (5) summary
      cd06263
      Location:422561
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:422563
      MAM; MAM domain, meprin/A5/mu
      pfam12662
      Location:150172
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:218253
      EGF_3; EGF domain
      cl00057
      Location:164204
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    2. NM_001184690.2NP_001171619.1  nephronectin isoform A precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes a protein (isoform A) of 582 amino acids.
      Source sequence(s)
      AC109361, AK295772, AW607534
      Consensus CDS
      CCDS54784.1
      UniProtKB/TrEMBL
      D6RH31
      Related
      ENSP00000402884.2, ENST00000453617.6
      Conserved Domains (6) summary
      cd06263
      Location:439578
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:439580
      MAM; MAM domain, meprin/A5/mu
      pfam07645
      Location:186218
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:167189
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:235270
      EGF_3; EGF domain
      cl00057
      Location:100142
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    3. NM_001184691.2NP_001171620.1  nephronectin isoform C precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences in the presence/absence of in-frame exons in the 5' coding region, compared to variant 1, and encodes a longer protein (isoform C), compared to isoform A.
      Source sequence(s)
      AC109361, AK295772, AK302477, AW607534
      Consensus CDS
      CCDS54785.1
      UniProtKB/TrEMBL
      D6RH31
      Related
      ENSP00000389252.2, ENST00000427316.6
      Conserved Domains (6) summary
      cd06263
      Location:452591
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:452593
      MAM; MAM domain, meprin/A5/mu
      pfam07645
      Location:199231
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:180202
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:248283
      EGF_3; EGF domain
      pfam14670
      Location:123157
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    4. NM_001184692.2NP_001171621.1  nephronectin isoform D precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks multiple in-frame exons in the coding region, compared to variant 1, and encodes a shorter protein (isoform D), compared to isoform A.
      Source sequence(s)
      AC109361, AK304279, AK304721, AW607534
      Consensus CDS
      CCDS54787.1
      UniProtKB/TrEMBL
      D6RH31
      Related
      ENSP00000422044.1, ENST00000514622.5
      Conserved Domains (5) summary
      cd06263
      Location:393532
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:393534
      MAM; MAM domain, meprin/A5/mu
      pfam12662
      Location:150172
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:218253
      EGF_3; EGF domain
      cl00057
      Location:164204
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    5. NM_001184693.2NP_001171622.1  nephronectin isoform E precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) has multiple differences in the presence/absence of in-frame exons in the coding region, compared to variant 1, and encodes a shorter protein (isoform E), compared to isoform A.
      Source sequence(s)
      AC109361, AK295772, AK304721, AW607534
      Consensus CDS
      CCDS54786.1
      UniProtKB/TrEMBL
      D6RH31
      Related
      ENSP00000422474.1, ENST00000506666.5
      Conserved Domains (6) summary
      cd06263
      Location:423562
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:423564
      MAM; MAM domain, meprin/A5/mu
      pfam12662
      Location:180202
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:248283
      EGF_3; EGF domain
      pfam14670
      Location:123157
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl00057
      Location:194234
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      105895471..105971671
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011531820.3XP_011530122.1  nephronectin isoform X1

      UniProtKB/TrEMBL
      D6RH31
      Conserved Domains (6) summary
      cd06263
      Location:470609
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:470611
      MAM; MAM domain, meprin/A5/mu
      pfam07645
      Location:217249
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:198220
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:266301
      EGF_3; EGF domain
      pfam14670
      Location:141175
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    2. XM_017007984.2XP_016863473.1  nephronectin isoform X9

      UniProtKB/TrEMBL
      H0YAK9
    3. XM_011531823.3XP_011530125.1  nephronectin isoform X4

      UniProtKB/TrEMBL
      D6RH31
      Conserved Domains (6) summary
      cd06263
      Location:441580
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:441582
      MAM; MAM domain, meprin/A5/mu
      pfam07645
      Location:217249
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:198220
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:266301
      EGF_3; EGF domain
      pfam14670
      Location:141175
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    4. XM_011531824.3XP_011530126.1  nephronectin isoform X5

      UniProtKB/TrEMBL
      D6RH31
      Conserved Domains (6) summary
      cd06263
      Location:440579
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:440581
      MAM; MAM domain, meprin/A5/mu
      pfam07645
      Location:187219
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:168190
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:236271
      EGF_3; EGF domain
      cl00057
      Location:101143
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    5. XM_047449983.1XP_047305939.1  nephronectin isoform X7

      UniProtKB/TrEMBL
      D6RH31
    6. XM_011531822.3XP_011530124.1  nephronectin isoform X3

      UniProtKB/TrEMBL
      D6RH31
      Conserved Domains (6) summary
      cd06263
      Location:453592
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:453594
      MAM; MAM domain, meprin/A5/mu
      pfam07645
      Location:200232
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:181203
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:249284
      EGF_3; EGF domain
      pfam14670
      Location:124158
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    7. XM_011531825.3XP_011530127.1  nephronectin isoform X6

      UniProtKB/TrEMBL
      D6RH31
      Conserved Domains (5) summary
      cd06263
      Location:423562
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:423564
      MAM; MAM domain, meprin/A5/mu
      pfam12662
      Location:151173
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:219254
      EGF_3; EGF domain
      cl00057
      Location:165205
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    8. XM_005262888.5XP_005262945.1  nephronectin isoform X2

      UniProtKB/TrEMBL
      D6RH31
      Related
      ENSP00000426146.1, ENST00000503451.5
      Conserved Domains (6) summary
      cd06263
      Location:469608
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      pfam00629
      Location:469610
      MAM; MAM domain, meprin/A5/mu
      pfam07645
      Location:216248
      EGF_CA; Calcium-binding EGF domain
      pfam12662
      Location:197219
      cEGF; Complement Clr-like EGF-like
      pfam12947
      Location:265300
      EGF_3; EGF domain
      pfam14670
      Location:140174
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    9. XM_047449985.1XP_047305941.1  nephronectin isoform X10

      UniProtKB/TrEMBL
      H0YAK9
    10. XM_047449984.1XP_047305940.1  nephronectin isoform X8

      UniProtKB/TrEMBL
      D6RH31
    11. XM_047449987.1XP_047305943.1  nephronectin isoform X12

      UniProtKB/TrEMBL
      H0YAK9
      Related
      ENSP00000427507.1, ENST00000514837.1
    12. XM_047449988.1XP_047305944.1  nephronectin isoform X13

      UniProtKB/TrEMBL
      H0YAK9
    13. XM_047449986.1XP_047305942.1  nephronectin isoform X11

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      109206597..109282798
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349545.1XP_054205520.1  nephronectin isoform X1

      UniProtKB/TrEMBL
      D6RH31
    2. XM_054349553.1XP_054205528.1  nephronectin isoform X9

      UniProtKB/TrEMBL
      H0YAK9
    3. XM_054349548.1XP_054205523.1  nephronectin isoform X4

      UniProtKB/TrEMBL
      D6RH31
    4. XM_054349549.1XP_054205524.1  nephronectin isoform X5

      UniProtKB/TrEMBL
      D6RH31
    5. XM_054349551.1XP_054205526.1  nephronectin isoform X7

      UniProtKB/TrEMBL
      D6RH31
    6. XM_054349547.1XP_054205522.1  nephronectin isoform X3

      UniProtKB/TrEMBL
      D6RH31
    7. XM_054349550.1XP_054205525.1  nephronectin isoform X6

      UniProtKB/TrEMBL
      D6RH31
    8. XM_054349546.1XP_054205521.1  nephronectin isoform X2

      UniProtKB/TrEMBL
      D6RH31
    9. XM_054349554.1XP_054205529.1  nephronectin isoform X10

      UniProtKB/TrEMBL
      H0YAK9
    10. XM_054349552.1XP_054205527.1  nephronectin isoform X8

      UniProtKB/TrEMBL
      D6RH31
    11. XM_054349556.1XP_054205531.1  nephronectin isoform X12

      UniProtKB/TrEMBL
      H0YAK9
    12. XM_054349557.1XP_054205532.1  nephronectin isoform X13

      UniProtKB/TrEMBL
      H0YAK9
    13. XM_054349555.1XP_054205530.1  nephronectin isoform X11

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_198278.1: Suppressed sequence

      Description
      NM_198278.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.