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    TENM3 teneurin transmembrane protein 3 [ Homo sapiens (human) ]

    Gene ID: 55714, updated on 5-Mar-2024

    Summary

    Official Symbol
    TENM3provided by HGNC
    Official Full Name
    teneurin transmembrane protein 3provided by HGNC
    Primary source
    HGNC:HGNC:29944
    See related
    Ensembl:ENSG00000218336 MIM:610083; AllianceGenome:HGNC:29944
    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
    ODZ3; TEN3; TNM3; ten-3; Ten-m3; MCOPCB9; MCOPS15
    Summary
    This gene encodes a member of the teneurin transmembrane protein family. The encoded protein may be involved in the regulation of neuronal development including development of the visual pathway. Mutations in this gene have been associated with microphthalmia and developmental dysplasia of the hip. [provided by RefSeq, Jan 2023]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Broad expression in placenta (RPKM 7.1), brain (RPKM 4.3) and 14 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TENM3 in Genome Data Viewer
    Location:
    4q34.3-q35.1
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (181447613..182803024)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (184789727..186144894)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (183164555..183724177)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:182199870-182200513 Neighboring gene NANOG hESC enhancer GRCh37_chr4:182230025-182230542 Neighboring gene long intergenic non-protein coding RNA 2500 Neighboring gene NANOG hESC enhancer GRCh37_chr4:182271856-182272545 Neighboring gene uncharacterized LOC107986205 Neighboring gene uncharacterized LOC124900822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:182353242-182353742 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:182470028-182471227 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:182509195-182509349 Neighboring gene epithelial cell adhesion molecule pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:182544780-182545979 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:182717259-182718458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22173 Neighboring gene TENM3 antisense transcript 2 Neighboring gene RN7SK pseudogene 13 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:182870312-182870817 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:182870818-182871322 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:182871323-182871827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:182930857-182931357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22175 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22176 Neighboring gene cyclin H pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:183005741-183006264 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:183006265-183006786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183062164-183062970 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:183065925-183066913 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:183110451-183111650 Neighboring gene uncharacterized LOC105377572 Neighboring gene TENM3 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:183128595-183128794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183129869-183130370 Neighboring gene microRNA 1305 Neighboring gene NANOG hESC enhancer GRCh37_chr4:183260333-183260928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15821 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76678 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:183481396-183482249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183492697-183493198 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:183506364-183506920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183514859-183515359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183546469-183546969 Neighboring gene RNA, U2 small nuclear 34, pseudogene Neighboring gene RN7SK pseudogene 67 Neighboring gene uncharacterized LOC105377571 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:183705545-183706046 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_76710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183728786-183729724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183729853-183730354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15824 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:183735292-183735847 Neighboring gene chr4 t(4;18)(q35;q18) HERV-H recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22177 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:183783101-183783676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183783677-183784250 Neighboring gene uncharacterized LOC105377576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:183816185-183816755 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:183818782-183819282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15825 Neighboring gene dCMP deaminase

    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

    Associated conditions

    Description Tests
    Microphthalmia, isolated, with coloboma 9
    MedGen: C3554592 OMIM: 615145 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association meta-analysis of preschool internalizing problems.
    EBI GWAS Catalog
    Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
    EBI GWAS Catalog
    Genome-wide association study of multiplex schizophrenia pedigrees.
    EBI GWAS Catalog
    Genome-wide association study of smoking behaviours among Bangladeshi adults.
    EBI GWAS Catalog
    Genome-wide meta-analysis of systolic blood pressure in children with sickle cell disease.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog
    No evidence of gene-calcium interactions from genome-wide analysis of colorectal cancer risk.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10474, FLJ10886, KIAA1455

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cell adhesion molecule binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein heterodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein heterodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein homodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in camera-type eye morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of homophilic cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in neuron projection IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    teneurin-3
    Names
    ODZ3-like protein
    odz, odd Oz/ten-m homolog 3
    protein Odd Oz/ten-m homolog 3
    tenascin-M3
    testicular tissue protein Li 195

    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.

    Genomic

    1. NG_042859.1 RefSeqGene

      Range
      4972..564594
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001080477.4NP_001073946.1  teneurin-3 isoform 1

      See identical proteins and their annotated locations for NP_001073946.1

      Status: REVIEWED

      Source sequence(s)
      AB040888, AC079226, AC131943, AF195420, AK001336
      Consensus CDS
      CCDS47165.1
      UniProtKB/Swiss-Prot
      Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273
      UniProtKB/TrEMBL
      A0A140VJW8
      Related
      ENSP00000424226.1, ENST00000511685.6
      Conserved Domains (11) summary
      COG3209
      Location:16132414
      RhsA; Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction only]
      cd00054
      Location:744773
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd05819
      Location:11751210
      NHL; NHL repeat [structural motif]
      TIGR01643
      Location:18231863
      YD_repeat_2x; YD repeat (two copies)
      TIGR03696
      Location:23182392
      Rhs_assc_core; RHS repeat-associated core domain
      pfam01500
      Location:579731
      Keratin_B2; Keratin, high sulfur B2 protein
      pfam06484
      Location:11308
      Ten_N; Teneurin Intracellular Region
      pfam07974
      Location:522544
      EGF_2; EGF-like domain
      pfam15636
      Location:26172692
      Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin
      cl18310
      Location:11461498
      NHL; NHL repeat unit of beta-propeller proteins
      cl19567
      Location:697738
      DSL; Delta serrate ligand
    2. NM_001415960.1NP_001402889.1  teneurin-3 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC109353, KF457841
    3. NM_001415961.1NP_001402890.1  teneurin-3 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC109353, KF457841
    4. NM_001415962.1NP_001402891.1  teneurin-3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC109353, KF457841
    5. NM_001415963.1NP_001402892.1  teneurin-3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC109353, KF457841
    6. NM_001415964.1NP_001402893.1  teneurin-3 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC109353, KF457841
    7. NM_001415966.1NP_001402895.1  teneurin-3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC108142, AC131943, KF457841
    8. NM_001415967.1NP_001402896.1  teneurin-3 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC108142, AC131943, KF457841
    9. NM_001415968.1NP_001402897.1  teneurin-3 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
    10. NM_001415969.1NP_001402898.1  teneurin-3 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
    11. NM_001415970.1NP_001402899.1  teneurin-3 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
    12. NM_001415971.1NP_001402900.1  teneurin-3 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
      UniProtKB/Swiss-Prot
      Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273
      UniProtKB/TrEMBL
      A0A140VJW8
    13. NM_001415973.1NP_001402902.1  teneurin-3 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
      UniProtKB/Swiss-Prot
      Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273
      UniProtKB/TrEMBL
      A0A140VJW8
    14. NM_001415974.1NP_001402903.1  teneurin-3 isoform 11

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
    15. NM_001415975.1NP_001402904.1  teneurin-3 isoform 11

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
    16. NM_001415976.1NP_001402905.1  teneurin-3 isoform 12

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC108142, AC131943, KF457841
    17. NM_001415977.1NP_001402906.1  teneurin-3 isoform 12

      Status: REVIEWED

      Source sequence(s)
      AC079226, AC105288, AC108142, AC131943, KF457841

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      181447613..182803024
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017008385.2XP_016863874.1  teneurin-3 isoform X1

      Conserved Domains (8) summary
      COG3209
      Location:17832338
      RhsA; Uncharacterized conserved protein RhsA, contains 28 RHS repeats [General function prediction only]
      cd05819
      Location:11841223
      NHL; NHL repeat [structural motif]
      TIGR03696
      Location:23342408
      Rhs_assc_core; RHS repeat-associated core domain
      cl18310
      Location:11551514
      NHL; NHL repeat unit of beta-propeller proteins
      pfam05593
      Location:16311662
      RHS_repeat; RHS Repeat
      pfam06484
      Location:11308
      Ten_N; Teneurin Intracellular Region
      pfam15636
      Location:26312708
      Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin
      NF033759
      Location:466801
      exchanger_TraA; outer membrane exchange protein TraA
    2. XM_017008389.2XP_016863878.1  teneurin-3 isoform X2

    3. XM_017008390.2XP_016863879.1  teneurin-3 isoform X3

    4. XM_017008391.2XP_016863880.1  teneurin-3 isoform X4

    5. XM_017008394.2XP_016863883.1  teneurin-3 isoform X7

    6. XM_047415944.1XP_047271900.1  teneurin-3 isoform X8

    7. XM_047415933.1XP_047271889.1  teneurin-3 isoform X1

    8. XM_017008386.2XP_016863875.1  teneurin-3 isoform X1

      Conserved Domains (8) summary
      COG3209
      Location:17832338
      RhsA; Uncharacterized conserved protein RhsA, contains 28 RHS repeats [General function prediction only]
      cd05819
      Location:11841223
      NHL; NHL repeat [structural motif]
      TIGR03696
      Location:23342408
      Rhs_assc_core; RHS repeat-associated core domain
      cl18310
      Location:11551514
      NHL; NHL repeat unit of beta-propeller proteins
      pfam05593
      Location:16311662
      RHS_repeat; RHS Repeat
      pfam06484
      Location:11308
      Ten_N; Teneurin Intracellular Region
      pfam15636
      Location:26312708
      Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin
      NF033759
      Location:466801
      exchanger_TraA; outer membrane exchange protein TraA
    9. XM_047415937.1XP_047271893.1  teneurin-3 isoform X5

    10. XM_017008387.3XP_016863876.1  teneurin-3 isoform X1

      Conserved Domains (8) summary
      COG3209
      Location:17832338
      RhsA; Uncharacterized conserved protein RhsA, contains 28 RHS repeats [General function prediction only]
      cd05819
      Location:11841223
      NHL; NHL repeat [structural motif]
      TIGR03696
      Location:23342408
      Rhs_assc_core; RHS repeat-associated core domain
      cl18310
      Location:11551514
      NHL; NHL repeat unit of beta-propeller proteins
      pfam05593
      Location:16311662
      RHS_repeat; RHS Repeat
      pfam06484
      Location:11308
      Ten_N; Teneurin Intracellular Region
      pfam15636
      Location:26312708
      Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin
      NF033759
      Location:466801
      exchanger_TraA; outer membrane exchange protein TraA
    11. XM_017008388.2XP_016863877.1  teneurin-3 isoform X1

      Conserved Domains (8) summary
      COG3209
      Location:17832338
      RhsA; Uncharacterized conserved protein RhsA, contains 28 RHS repeats [General function prediction only]
      cd05819
      Location:11841223
      NHL; NHL repeat [structural motif]
      TIGR03696
      Location:23342408
      Rhs_assc_core; RHS repeat-associated core domain
      cl18310
      Location:11551514
      NHL; NHL repeat unit of beta-propeller proteins
      pfam05593
      Location:16311662
      RHS_repeat; RHS Repeat
      pfam06484
      Location:11308
      Ten_N; Teneurin Intracellular Region
      pfam15636
      Location:26312708
      Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin
      NF033759
      Location:466801
      exchanger_TraA; outer membrane exchange protein TraA
    12. XM_047415940.1XP_047271896.1  teneurin-3 isoform X6

      UniProtKB/Swiss-Prot
      Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273
      UniProtKB/TrEMBL
      A0A140VJW8
    13. XM_047415948.1XP_047271904.1  teneurin-3 isoform X10

    14. XM_017008395.2XP_016863884.1  teneurin-3 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      184789727..186144894
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350462.1XP_054206437.1  teneurin-3 isoform X1

    2. XM_054350467.1XP_054206442.1  teneurin-3 isoform X2

    3. XM_054350468.1XP_054206443.1  teneurin-3 isoform X3

    4. XM_054350469.1XP_054206444.1  teneurin-3 isoform X4

    5. XM_054350472.1XP_054206447.1  teneurin-3 isoform X7

    6. XM_054350473.1XP_054206448.1  teneurin-3 isoform X8

    7. XM_054350465.1XP_054206440.1  teneurin-3 isoform X1

    8. XM_054350463.1XP_054206438.1  teneurin-3 isoform X1

    9. XM_054350470.1XP_054206445.1  teneurin-3 isoform X5

    10. XM_054350464.1XP_054206439.1  teneurin-3 isoform X1

    11. XM_054350466.1XP_054206441.1  teneurin-3 isoform X1

    12. XM_054350471.1XP_054206446.1  teneurin-3 isoform X6

      UniProtKB/Swiss-Prot
      Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273
      UniProtKB/TrEMBL
      A0A140VJW8
    13. XM_054350475.1XP_054206450.1  teneurin-3 isoform X10

    14. XM_054350474.1XP_054206449.1  teneurin-3 isoform X9