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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
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Genomic context

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