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RNF38 ring finger protein 38 [ Homo sapiens (human) ]

Gene ID: 152006, updated on 5-Mar-2024

Summary

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Official Symbol
RNF38provided by HGNC
Official Full Name
ring finger protein 38provided by HGNC
Primary source
HGNC:HGNC:18052
See related
Ensembl:ENSG00000137075 MIM:612488; AllianceGenome:HGNC:18052
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
Summary
This gene encodes a protein with a coiled-coil motif and a RING-H2 motif (C3H2C2) at its carboxy-terminus. The RING motif is a zinc-binding domain found in a large set of proteins playing roles in diverse cellular processes including oncogenesis, development, signal transduction, and apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
Expression
Ubiquitous expression in testis (RPKM 25.8), ovary (RPKM 14.9) and 25 other tissues See more
Orthologs
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Genomic context

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See RNF38 in Genome Data Viewer
Location:
9p13.2
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (36336400..36487669, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (36358438..36510372, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (36336397..36401203, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902150 Neighboring gene uncharacterized LOC102724322 Neighboring gene glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase Neighboring gene RNA, U4 small nuclear 53, pseudogene Neighboring gene high mobility group box 3 pseudogene 24 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36391761-36392261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19893 Neighboring gene uncharacterized LOC124902152 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:36415685-36416307 Neighboring gene mitochondrial ribosomal protein S21 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28352 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:36482565-36482744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28354 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:36558262-36558872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36571611-36572110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36584821-36585797 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:36596422-36596589 Neighboring gene maternal embryonic leucine zipper kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36725931-36726432 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:36738402-36739601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19897 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:36756569-36756775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36764310-36764828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36764829-36765347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28356 Neighboring gene uncharacterized LOC105376030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36820286-36820786 Neighboring gene microRNA 4475

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. Cloning and characterization of a novel human gene RNF38 encoding a conserved putative protein with a RING finger domain. Eisenberg I, et al. Biochem Biophys Res Commun, 2002 Jun 28. PMID 12074600
  2. Hsa_circ_0097009 regulates proliferation, apoptosis, migration and invasion of hepatocellular carcinoma cells via miR-568/RNF38 axis. Wu Z, et al. Bratisl Lek Listy, 2023. PMID 36598315
  3. RNF38 inhibits osteosarcoma cell proliferation by binding to CRY1. Zhou J, et al. Biochem Cell Biol, 2021 Oct. PMID 34460347
  4. Inhibiting microRNA-301b suppresses cell growth and targets RNF38 in cervical carcinoma. Guo WL, et al. Kaohsiung J Med Sci, 2020 Nov. PMID 32643846
  5. RING Finger Protein 38 Mediates LIM Domain Binding 1 Degradation and Regulates Cell Growth in Colorectal Cancer. Huang Z, et al. Onco Targets Ther, 2020. PMID 32021282, Free PMC Article

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Hsa_circ_0097009 regulates proliferation, apoptosis, migration and invasion of hepatocellular carcinoma cells via miR-568/RNF38 axis.
    Title: Hsa_circ_0097009 regulates proliferation, apoptosis, migration and invasion of hepatocellular carcinoma cells via miR-568/RNF38 axis.
  2. RNF38 suppress growth and metastasis via ubiquitination of ACTN4 in nasopharyngeal carcinoma.
    Title: RNF38 suppress growth and metastasis via ubiquitination of ACTN4 in nasopharyngeal carcinoma.
  3. RNF38 inhibits osteosarcoma cell proliferation by binding to CRY1.
    Title: RNF38 inhibits osteosarcoma cell proliferation by binding to CRY1.
  4. Inhibiting microRNA-301b suppresses cell growth and targets RNF38 in cervical carcinoma.
    Title: Inhibiting microRNA-301b suppresses cell growth and targets RNF38 in cervical carcinoma.
  5. Long non-coding RNA SNHG5 promotes human hepatocellular carcinoma progression by regulating miR-363-3p/RNF38 axis.
    Title: Long non-coding RNA SNHG5 promotes human hepatocellular carcinoma progression by regulating miR-363-3p/RNF38 axis.
  6. Data show that E3 ubiquitin-protein ligase RNF38 (RNF38) interacts with the nonreceptor tyrosine phosphatase SH2-containing protein tyrosine phosphatase 1 (SHP-1) and induces the polyubiquitination of SHP-1, which leads to destabilization of SHP-1.
    Title: RING finger protein 38 induces gastric cancer cell growth by decreasing the stability of the protein tyrosine phosphatase SHP-1.
  7. AHNAK interference restored the hepatocellular carcinoma (HCC) cell invasion and metastasis deprived by RNF38 downregulation. Clinically, elevated RNF38 and transforming growth factor beta receptor 1 (TGFBR1) expression was related to short overall survival (OS) and high cumulative recurrence rates in HCC patients.
    Title: Overexpression of RNF38 facilitates TGF-β signaling by Ubiquitinating and degrading AHNAK in hepatocellular carcinoma.
  8. identified RNF38 as a novel E3 ligase that modifies RUNX1 function without inducing its degradation
    Title: The ubiquitin ligase RNF38 promotes RUNX1 ubiquitination and enhances RUNX1-mediated suppression of erythroid transcription program.
  9. These results suggest RNF38 is an E3 ubiquitin ligase that may play a role in regulating p53.
    Title: RNF38 encodes a nuclear ubiquitin protein ligase that modifies p53.
  10. Cloning and characterization of the RNF38 gene
    Title: Cloning and characterization of a novel human gene RNF38 encoding a conserved putative protein with a RING finger domain.
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

  • FLJ21343

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in male gonad development IEA
Inferred from Electronic Annotation
more info
  
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in sperm flagellum IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
E3 ubiquitin-protein ligase RNF38
Names
RING-type E3 ubiquitin transferase RNF38
NP_073618.3
NP_919309.1
NP_919310.1
NP_919311.1
NP_919313.1
XP_005251423.1
XP_005251424.1
XP_006716784.1
XP_011516014.1
XP_011516015.1
XP_016869783.1
XP_016869785.1
XP_016869786.1
XP_047278750.1
XP_047278751.1
XP_047278752.1
XP_047278753.1
XP_047278754.1
XP_047278755.1
XP_047278756.1
XP_047278757.1
XP_047278758.1
XP_047278759.1
XP_047278760.1
XP_047278761.1
XP_047278762.1
XP_054217976.1
XP_054217977.1
XP_054217978.1
XP_054217979.1
XP_054217980.1
XP_054217981.1
XP_054217982.1
XP_054217983.1
XP_054217984.1
XP_054217985.1
XP_054217986.1
XP_054217987.1
XP_054217988.1
XP_054217989.1
XP_054217990.1
XP_054217991.1
XP_054217992.1
XP_054217993.1
XP_054217994.1
XP_054217995.1

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_022781.5 → NP_073618.3  E3 ubiquitin-protein ligase RNF38 isoform 1

    See identical proteins and their annotated locations for NP_073618.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF394047, AL120640, AL136817, AL161792, BC033786
    Consensus CDS
    CCDS6603.1
    UniProtKB/Swiss-Prot
    A6PVP9, B1AM81, B1AM82, B3KSG4, E7EVL3, Q7LB33, Q8N0Y0, Q9H0F5, Q9H748
    Related
    ENSP00000259605.6, ENST00000259605.11
    Conserved Domains (1) summary
    cd16472
    Location:460 → 504
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  2. NM_194328.3 → NP_919309.1  E3 ubiquitin-protein ligase RNF38 isoform 2

    See identical proteins and their annotated locations for NP_919309.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' terminal exon compared to variant 1. This difference causes translation initiation at a downstream AUG and an isoform (2) with a shorter N-terminus compared to isoform 1. Variants 2, 5 and 6 encode the same isoform.
    Source sequence(s)
    AF394047, AL161792, AL354935, BG722531, BI459742
    UniProtKB/Swiss-Prot
    Q9H0F5
    Related
    ENSP00000349566.3, ENST00000357058.7
    Conserved Domains (1) summary
    cd16472
    Location:377 → 421
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  3. NM_194329.3 → NP_919310.1  E3 ubiquitin-protein ligase RNF38 isoform 3

    See identical proteins and their annotated locations for NP_919310.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AF394047, AL120640, AL161792, BC033786
    Consensus CDS
    CCDS6604.1
    UniProtKB/Swiss-Prot
    Q9H0F5
    Related
    ENSP00000335239.5, ENST00000353739.8
    Conserved Domains (1) summary
    cd16472
    Location:410 → 454
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  4. NM_194330.3 → NP_919311.1  E3 ubiquitin-protein ligase RNF38 isoform 2

    See identical proteins and their annotated locations for NP_919311.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has an alternate 5' terminal exon compared to variant 1. This difference causes translation initiation at a downstream AUG and an isoform (2) with a shorter N-terminus compared to isoform 1. Variants 2, 5 and 6 encode the same isoform.
    Source sequence(s)
    AF394047, AL161792, AL354935, BC033786, BI520161, DA483270
    UniProtKB/Swiss-Prot
    Q9H0F5
    Related
    ENSP00000367117.2, ENST00000377885.6
    Conserved Domains (1) summary
    cd16472
    Location:377 → 421
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  5. NM_194332.3 → NP_919313.1  E3 ubiquitin-protein ligase RNF38 isoform 2

    See identical proteins and their annotated locations for NP_919313.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has an alternate 5' terminal exon and lacks an exon compared to variant 1. These differences cause translation initiation at a downstream AUG and an isoform (2) with a shorter N-terminus compared to isoform 1. Variants 2, 5 and 6 encode the same isoform.
    Source sequence(s)
    AF394047, AL161792, AL354935, BG722531, BI459742, DA189510
    UniProtKB/Swiss-Prot
    Q9H0F5
    Related
    ENSP00000343947.4, ENST00000350199.8
    Conserved Domains (1) summary
    cd16472
    Location:377 → 421
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

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
    36336400..36487669 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422796.1 → XP_047278752.1  E3 ubiquitin-protein ligase RNF38 isoform X3

  2. XM_047422795.1 → XP_047278751.1  E3 ubiquitin-protein ligase RNF38 isoform X2

  3. XM_047422794.1 → XP_047278750.1  E3 ubiquitin-protein ligase RNF38 isoform X1

  4. XM_017014296.2 → XP_016869785.1  E3 ubiquitin-protein ligase RNF38 isoform X7

    Conserved Domains (1) summary
    cd16472
    Location:347 → 391
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  5. XM_011517712.3 → XP_011516014.1  E3 ubiquitin-protein ligase RNF38 isoform X6

    See identical proteins and their annotated locations for XP_011516014.1

    UniProtKB/Swiss-Prot
    Q9H0F5
    Conserved Domains (1) summary
    cd16472
    Location:377 → 421
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  6. XM_017014297.2 → XP_016869786.1  E3 ubiquitin-protein ligase RNF38 isoform X7

    Conserved Domains (1) summary
    cd16472
    Location:347 → 391
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  7. XM_047422803.1 → XP_047278759.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  8. XM_017014294.2 → XP_016869783.1  E3 ubiquitin-protein ligase RNF38 isoform X5

  9. XM_047422802.1 → XP_047278758.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  10. XM_047422805.1 → XP_047278761.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  11. XM_006716721.4 → XP_006716784.1  E3 ubiquitin-protein ligase RNF38 isoform X6

    See identical proteins and their annotated locations for XP_006716784.1

    UniProtKB/Swiss-Prot
    Q9H0F5
    Conserved Domains (1) summary
    cd16472
    Location:377 → 421
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  12. XM_005251367.4 → XP_005251424.1  E3 ubiquitin-protein ligase RNF38 isoform X6

    See identical proteins and their annotated locations for XP_005251424.1

    UniProtKB/Swiss-Prot
    Q9H0F5
    Conserved Domains (1) summary
    cd16472
    Location:377 → 421
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  13. XM_005251366.4 → XP_005251423.1  E3 ubiquitin-protein ligase RNF38 isoform X6

    See identical proteins and their annotated locations for XP_005251423.1

    UniProtKB/Swiss-Prot
    Q9H0F5
    Conserved Domains (1) summary
    cd16472
    Location:377 → 421
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  14. XM_011517713.3 → XP_011516015.1  E3 ubiquitin-protein ligase RNF38 isoform X6

    See identical proteins and their annotated locations for XP_011516015.1

    UniProtKB/Swiss-Prot
    Q9H0F5
    Conserved Domains (1) summary
    cd16472
    Location:377 → 421
    RING-H2_RNF38_like; RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins

  15. XM_047422801.1 → XP_047278757.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  16. XM_047422804.1 → XP_047278760.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  17. XM_047422800.1 → XP_047278756.1  E3 ubiquitin-protein ligase RNF38 isoform X6

    Related
    ENSP00000483536.1, ENST00000611646.4

  18. XM_047422797.1 → XP_047278753.1  E3 ubiquitin-protein ligase RNF38 isoform X4

  19. XM_047422799.1 → XP_047278755.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  20. XM_047422798.1 → XP_047278754.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  21. XM_047422806.1 → XP_047278762.1  E3 ubiquitin-protein ligase RNF38 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    36358438..36510372 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362003.1 → XP_054217978.1  E3 ubiquitin-protein ligase RNF38 isoform X3

  2. XM_054362001.1 → XP_054217976.1  E3 ubiquitin-protein ligase RNF38 isoform X1

  3. XM_054362002.1 → XP_054217977.1  E3 ubiquitin-protein ligase RNF38 isoform X2

  4. XM_054362018.1 → XP_054217993.1  E3 ubiquitin-protein ligase RNF38 isoform X7

  5. XM_054362019.1 → XP_054217994.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  6. XM_054362017.1 → XP_054217992.1  E3 ubiquitin-protein ligase RNF38 isoform X7

  7. XM_054362014.1 → XP_054217989.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  8. XM_054362005.1 → XP_054217980.1  E3 ubiquitin-protein ligase RNF38 isoform X5

  9. XM_054362013.1 → XP_054217988.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  10. XM_054362015.1 → XP_054217990.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  11. XM_054362009.1 → XP_054217984.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  12. XM_054362007.1 → XP_054217982.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  13. XM_054362008.1 → XP_054217983.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  14. XM_054362006.1 → XP_054217981.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  15. XM_054362016.1 → XP_054217991.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  16. XM_054362011.1 → XP_054217986.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  17. XM_054362004.1 → XP_054217979.1  E3 ubiquitin-protein ligase RNF38 isoform X4

  18. XM_054362012.1 → XP_054217987.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  19. XM_054362010.1 → XP_054217985.1  E3 ubiquitin-protein ligase RNF38 isoform X6

  20. XM_054362020.1 → XP_054217995.1  E3 ubiquitin-protein ligase RNF38 isoform X6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_194331.1: Suppressed sequence

    Description
    NM_194331.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H0F5.4 GenPept UniProtKB/Swiss-Prot:Q9H0F5

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