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    FREM1 FRAS1 related extracellular matrix 1 [ Homo sapiens (human) ]

    Gene ID: 158326, updated on 3-Apr-2024

    Summary

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    Official Symbol
    FREM1provided by HGNC
    Official Full Name
    FRAS1 related extracellular matrix 1provided by HGNC
    Primary source
    HGNC:HGNC:23399
    See related
    Ensembl:ENSG00000164946 MIM:608944; AllianceGenome:HGNC:23399
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BNAR; MOTA; TILRR; TRIGNO2; C9orf143; C9orf145; C9orf154
    Summary
    This gene encodes a basement membrane protein that may play a role in craniofacial and renal development. Mutations in this gene have been associated with bifid nose with or without anorectal and renal anomalies. Alternatively spliced transcript variants encoding different isoforms have been described. PubMed ID 19940113 describes one such variant that initiates transcription within a distinct, internal exon; the resulting shorter isoform (named Toll-like/interleukin-1 receptor regulator, TILRR) is suggested to be a co-receptor of the interleukin 1 receptor family and may regulate receptor function and Toll-like receptor/interleukin 1 receptor signal transduction, contributing to the control of inflammatory response activation. [provided by RefSeq, Apr 2011]
    Expression
    Broad expression in endometrium (RPKM 5.0), kidney (RPKM 2.2) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9p22.3
    Exon count:
    46
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (14737152..14910995, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (14746865..14921449, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (14737150..14910993, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:14597299-14597830 Neighboring gene zinc finger DHHC-type palmitoyltransferase 21 Neighboring gene cell division cycle associated 4 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19776 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:14693435-14693935 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:14721879-14722818 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:14722819-14723756 Neighboring gene cerberus 1, DAN family BMP antagonist Neighboring gene uncharacterized LOC105375979 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:14812530-14813729 Neighboring gene RNA, U6 small nuclear 1260, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:14907200-14907740 Neighboring gene NANOG hESC enhancer GRCh37_chr9:14908690-14909191 Neighboring gene uncharacterized LOC124902122 Neighboring gene lactate dehydrogenase A pseudogene 4

    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. High level of plasma TILRR protein is associated with faster HIV seroconversion. Kashem MA, et al. EBioMedicine, 2022 Apr. PMID 35339895, Free PMC Article
    2. Elevated expression of FREM1 in breast cancer indicates favorable prognosis and high-level immune infiltration status. Li HN, et al. Cancer Med, 2020 Dec. PMID 33058542, Free PMC Article
    3. Heterozygous intragenic deletions of FREM1 are not associated with trigonocephaly. Dawson AJ, et al. Clin Dysmorphol, 2021 Apr 1. PMID 33038106
    4. Bifid nose as the sole manifestation of BNAR syndrome, a FREM1-related condition. Brischoux-Boucher E, et al. Clin Genet, 2020 Nov. PMID 32926405
    5. Toll-like Interleukin 1 Receptor Regulator Is an Important Modulator of Inflammation Responsive Genes. Kashem MA, et al. Front Immunol, 2019. PMID 30873160, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Two novel mutations within FREM1 gene in patients with bifid nose.
      Title: Two novel mutations within FREM1 gene in patients with bifid nose.
    2. High level of plasma TILRR protein is associated with faster HIV seroconversion.
      Title: High level of plasma TILRR protein is associated with faster HIV seroconversion.
    3. Heterozygous intragenic deletions of FREM1 are not associated with trigonocephaly.
      Title: Heterozygous intragenic deletions of FREM1 are not associated with trigonocephaly.
    4. Bifid nose as the sole manifestation of BNAR syndrome, a FREM1-related condition.
      Title: Bifid nose as the sole manifestation of BNAR syndrome, a FREM1-related condition.
    5. Elevated expression of FREM1 in breast cancer indicates favorable prognosis and high-level immune infiltration status.
      Title: Elevated expression of FREM1 in breast cancer indicates favorable prognosis and high-level immune infiltration status.
    6. Toll-like Interleukin 1 Receptor Regulator Is an Important Modulator of Inflammation Responsive Genes.
      Title: Toll-like Interleukin 1 Receptor Regulator Is an Important Modulator of Inflammation Responsive Genes.
    7. Our results showed that p.Arg2167Trp had a weaker effect in interrupting interactions between FREM2 and FREM1 than FS-associated missense mutation p.Glu1972Lys. Overall, our data demonstrate that the homozygous mutation p.Arg2167Trp in FREM2 causes isolated Cryptophthalmos(CO), which will facilitate our better understanding of the molecular mechanisms underlying the disease
      Title: A homozygous mutation p.Arg2167Trp in FREM2 causes isolated cryptophthalmos.
    8. we identified genome-wide significant association involving measures of central upper lip height at 9p22 within FREM1
      Title: Genome-wide association study of facial morphology reveals novel associations with FREM1 and PARK2.
    9. FREM1 expression is significantly downregulated in human masticatory mucosa during wound healing
      Title: Human gingiva transcriptome during wound healing.
    10. this report describes a patient with a phenotype compatible with Manitoba-oculo-tricho-anal syndrome in whom two novel FREM1 mutations were identified in the compound heterozygous state thus broadening the mutational spectrum of the disease.
      Title: Novel FREM1 mutations in a patient with MOTA syndrome: Clinical findings, mutation update and review of FREM1-related disorders literature.
    Submit: New GeneRIF Correction See all GeneRIFs (23)

    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

    Associated conditions

    Description Tests
    BNAR syndrome
    MedGen: C2750433 OMIM: 608980 GeneReviews: FREM1 Autosomal Recessive Disorders
    		Compare labs
    Oculotrichoanal syndrome
    MedGen: C1855425 OMIM: 248450 GeneReviews: FREM1 Autosomal Recessive Disorders
    		Compare labs
    Trigonocephaly 2
    MedGen: C3280974 OMIM: 614485 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Identification of 15 loci influencing height in a Korean population.
    EBI GWAS Catalog

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25461

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in anatomical structure morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell communication IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-matrix adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in craniofacial suture morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in basement membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    FRAS1-related extracellular matrix protein 1
    Names
    extracellular matrix protein QBRICK

    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.

    Genomic

    1. NG_017005.2 RefSeqGene

      Range
      4809..178085
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001177704.3 → NP_001171175.1  FRAS1-related extracellular matrix protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001171175.1

      Status: REVIEWED

      Source sequence(s)
      AL390732, AL512643
      Consensus CDS
      CCDS55293.1
      UniProtKB/Swiss-Prot
      Q5H8C1
      Related
      ENSP00000370278.1, ENST00000380894.5
      Conserved Domains (3) summary
      smart00034
      Location:589 → 711
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:25 → 134
      Cadherin_3; Cadherin-like
      cl02522
      Location:282 → 365
      Calx-beta; Calx-beta domain

    2. NM_001370058.2 → NP_001356987.1  FRAS1-related extracellular matrix protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL390732, AL512643
      Conserved Domains (1) summary
      cl02522
      Location:282 → 340
      Calx-beta; Calx-beta domain

    3. NM_001370060.1 → NP_001356989.1  FRAS1-related extracellular matrix protein 1 isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL354672, AL512643
      Conserved Domains (1) summary
      pfam16184
      Location:324 → 400
      Cadherin_3; Cadherin-like

    4. NM_001370061.2 → NP_001356990.1  FRAS1-related extracellular matrix protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL390732, AL512643
      Consensus CDS
      CCDS55293.1
      Conserved Domains (3) summary
      smart00034
      Location:589 → 711
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:25 → 134
      Cadherin_3; Cadherin-like
      cl02522
      Location:282 → 365
      Calx-beta; Calx-beta domain

    5. NM_001370063.1 → NP_001356992.1  FRAS1-related extracellular matrix protein 1 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variant 7, encodes isoform 5.
      Source sequence(s)
      AL354672, AL512643
      Conserved Domains (1) summary
      pfam16184
      Location:315 → 391
      Cadherin_3; Cadherin-like

    6. NM_001370065.1 → NP_001356994.1  FRAS1-related extracellular matrix protein 1 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7), as well as variant 6, encodes isoform 5.
      Source sequence(s)
      AL354672, AL512643
      Conserved Domains (1) summary
      pfam16184
      Location:315 → 391
      Cadherin_3; Cadherin-like

    7. NM_001379081.2 → NP_001366010.1  FRAS1-related extracellular matrix protein 1 isoform 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AL354672, AL390732, AL512643
      Consensus CDS
      CCDS47952.1
      UniProtKB/Swiss-Prot
      B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3
      Related
      ENSP00000370262.3, ENST00000380880.4
      Conserved Domains (3) summary
      smart00034
      Location:2053 → 2175
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:1489 → 1598
      Cadherin_3; Cadherin-like
      cl02522
      Location:1746 → 1829
      Calx-beta; Calx-beta domain

    8. NM_144966.7 → NP_659403.4  FRAS1-related extracellular matrix protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_659403.4

      Status: REVIEWED

      Source sequence(s)
      AL354672, AL390732, AL512643
      Consensus CDS
      CCDS47952.1
      UniProtKB/Swiss-Prot
      B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3
      Conserved Domains (3) summary
      smart00034
      Location:2053 → 2175
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:1489 → 1598
      Cadherin_3; Cadherin-like
      cl02522
      Location:1746 → 1829
      Calx-beta; Calx-beta domain

    RNA

    1. NR_163238.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL354672, AL390732, AL512643
      Related
      ENST00000380875.7

    2. NR_163239.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL354672, AL390732, AL512643

    3. NR_163240.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL354672, AL512643

    4. NR_163241.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL354672, AL512643

    5. NR_163242.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL390732, AL512643

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      14737152..14910995 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422844.1 → XP_047278800.1  FRAS1-related extracellular matrix protein 1 isoform X1

    2. XM_047422847.1 → XP_047278803.1  FRAS1-related extracellular matrix protein 1 isoform X2

      UniProtKB/Swiss-Prot
      B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3

    3. XM_017014322.2 → XP_016869811.1  FRAS1-related extracellular matrix protein 1 isoform X1

    4. XM_047422846.1 → XP_047278802.1  FRAS1-related extracellular matrix protein 1 isoform X2

      UniProtKB/Swiss-Prot
      B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3

    5. XM_017014321.3 → XP_016869810.1  FRAS1-related extracellular matrix protein 1 isoform X1

    6. XM_017014324.3 → XP_016869813.1  FRAS1-related extracellular matrix protein 1 isoform X3

    7. XM_017014325.3 → XP_016869814.1  FRAS1-related extracellular matrix protein 1 isoform X4

    8. XM_017014316.3 → XP_016869805.1  FRAS1-related extracellular matrix protein 1 isoform X1

    9. XM_047422848.1 → XP_047278804.1  FRAS1-related extracellular matrix protein 1 isoform X2

      UniProtKB/Swiss-Prot
      B7ZBX4, Q5H8C1, Q5VV00, Q5VV01, Q6MZI4, Q8NEG9, Q96LI3

    10. XM_017014320.3 → XP_016869809.1  FRAS1-related extracellular matrix protein 1 isoform X1

    11. XM_017014319.3 → XP_016869808.1  FRAS1-related extracellular matrix protein 1 isoform X1

    12. XM_047422845.1 → XP_047278801.1  FRAS1-related extracellular matrix protein 1 isoform X1

    13. XM_017014326.2 → XP_016869815.1  FRAS1-related extracellular matrix protein 1 isoform X5

    14. XM_017014327.3 → XP_016869816.1  FRAS1-related extracellular matrix protein 1 isoform X6

    15. XM_006716729.4 → XP_006716792.1  FRAS1-related extracellular matrix protein 1 isoform X19

      See identical proteins and their annotated locations for XP_006716792.1

      UniProtKB/Swiss-Prot
      Q5H8C1
      Conserved Domains (3) summary
      smart00034
      Location:589 → 711
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:25 → 134
      Cadherin_3; Cadherin-like
      cl02522
      Location:282 → 365
      Calx-beta; Calx-beta domain

    16. XM_047422859.1 → XP_047278815.1  FRAS1-related extracellular matrix protein 1 isoform X20

    17. XM_011517758.3 → XP_011516060.1  FRAS1-related extracellular matrix protein 1 isoform X18

      Conserved Domains (3) summary
      smart00034
      Location:601 → 723
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      pfam16184
      Location:115 → 273
      Cadherin_3; Cadherin-like
      cl02522
      Location:294 → 377
      Calx-beta; Calx-beta domain

    18. XM_017014329.3 → XP_016869818.1  FRAS1-related extracellular matrix protein 1 isoform X8

    19. XM_017014328.3 → XP_016869817.1  FRAS1-related extracellular matrix protein 1 isoform X7

    20. XM_047422852.1 → XP_047278808.1  FRAS1-related extracellular matrix protein 1 isoform X12

    21. XM_047422851.1 → XP_047278807.1  FRAS1-related extracellular matrix protein 1 isoform X11

    22. XM_047422850.1 → XP_047278806.1  FRAS1-related extracellular matrix protein 1 isoform X10

    23. XM_047422849.1 → XP_047278805.1  FRAS1-related extracellular matrix protein 1 isoform X9

    24. XM_047422854.1 → XP_047278810.1  FRAS1-related extracellular matrix protein 1 isoform X14

    25. XM_047422853.1 → XP_047278809.1  FRAS1-related extracellular matrix protein 1 isoform X13

    26. XM_047422858.1 → XP_047278814.1  FRAS1-related extracellular matrix protein 1 isoform X17

    27. XM_047422857.1 → XP_047278813.1  FRAS1-related extracellular matrix protein 1 isoform X17

    28. XM_047422856.1 → XP_047278812.1  FRAS1-related extracellular matrix protein 1 isoform X17

    29. XM_047422855.1 → XP_047278811.1  FRAS1-related extracellular matrix protein 1 isoform X15

    30. XM_017014330.3 → XP_016869819.1  FRAS1-related extracellular matrix protein 1 isoform X16

      UniProtKB/TrEMBL
      F8WE85

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      14746865..14921449 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362116.1 → XP_054218091.1  FRAS1-related extracellular matrix protein 1 isoform X1

    2. XM_054362110.1 → XP_054218085.1  FRAS1-related extracellular matrix protein 1 isoform X1

    3. XM_054362111.1 → XP_054218086.1  FRAS1-related extracellular matrix protein 1 isoform X1

    4. XM_054362115.1 → XP_054218090.1  FRAS1-related extracellular matrix protein 1 isoform X1

    5. XM_054362118.1 → XP_054218093.1  FRAS1-related extracellular matrix protein 1 isoform X2

    6. XM_054362117.1 → XP_054218092.1  FRAS1-related extracellular matrix protein 1 isoform X2

    7. XM_054362114.1 → XP_054218089.1  FRAS1-related extracellular matrix protein 1 isoform X1

    8. XM_054362120.1 → XP_054218095.1  FRAS1-related extracellular matrix protein 1 isoform X3

    9. XM_054362121.1 → XP_054218096.1  FRAS1-related extracellular matrix protein 1 isoform X4

    10. XM_054362109.1 → XP_054218084.1  FRAS1-related extracellular matrix protein 1 isoform X1

    11. XM_054362119.1 → XP_054218094.1  FRAS1-related extracellular matrix protein 1 isoform X2

    12. XM_054362113.1 → XP_054218088.1  FRAS1-related extracellular matrix protein 1 isoform X1

    13. XM_054362112.1 → XP_054218087.1  FRAS1-related extracellular matrix protein 1 isoform X1

    14. XM_054362122.1 → XP_054218097.1  FRAS1-related extracellular matrix protein 1 isoform X5

    15. XM_054362123.1 → XP_054218098.1  FRAS1-related extracellular matrix protein 1 isoform X6

    16. XM_054362138.1 → XP_054218113.1  FRAS1-related extracellular matrix protein 1 isoform X19

    17. XM_054362139.1 → XP_054218114.1  FRAS1-related extracellular matrix protein 1 isoform X20

    18. XM_054362137.1 → XP_054218112.1  FRAS1-related extracellular matrix protein 1 isoform X18

    19. XM_054362125.1 → XP_054218100.1  FRAS1-related extracellular matrix protein 1 isoform X8

    20. XM_054362124.1 → XP_054218099.1  FRAS1-related extracellular matrix protein 1 isoform X7

    21. XM_054362129.1 → XP_054218104.1  FRAS1-related extracellular matrix protein 1 isoform X12

    22. XM_054362128.1 → XP_054218103.1  FRAS1-related extracellular matrix protein 1 isoform X11

    23. XM_054362127.1 → XP_054218102.1  FRAS1-related extracellular matrix protein 1 isoform X10

    24. XM_054362126.1 → XP_054218101.1  FRAS1-related extracellular matrix protein 1 isoform X9

    25. XM_054362131.1 → XP_054218106.1  FRAS1-related extracellular matrix protein 1 isoform X14

    26. XM_054362130.1 → XP_054218105.1  FRAS1-related extracellular matrix protein 1 isoform X13

    27. XM_054362136.1 → XP_054218111.1  FRAS1-related extracellular matrix protein 1 isoform X17

    28. XM_054362135.1 → XP_054218110.1  FRAS1-related extracellular matrix protein 1 isoform X17

    29. XM_054362134.1 → XP_054218109.1  FRAS1-related extracellular matrix protein 1 isoform X17

    30. XM_054362132.1 → XP_054218107.1  FRAS1-related extracellular matrix protein 1 isoform X15

    31. XM_054362133.1 → XP_054218108.1  FRAS1-related extracellular matrix protein 1 isoform X16

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5H8C1.3 GenPept UniProtKB/Swiss-Prot:Q5H8C1

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