Human Gene MTA3 (ENST00000405094.2_12) from GENCODE V47lift37

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Description: metastasis associated 1 family member 3, transcript variant 6 (from RefSeq NM_001330444.2)
Gencode Transcript: ENST00000405094.2_12
Gencode Gene: ENSG00000057935.14_13
Transcript (Including UTRs)
Position: hg19 chr2:42,795,772-42,984,086 Size: 188,315 Total Exon Count: 17 Strand: +
Coding Region
Position: hg19 chr2:42,795,886-42,980,539 Size: 184,654 Coding Exon Count: 17

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr2:42,795,772-42,984,086)			mRNA (may differ from genome)		Protein (594 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: MTA3_HUMAN DESCRIPTION: RecName: Full=Metastasis-associated protein MTA3; FUNCTION: Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. SUBUNIT: Component of the nucleosome-remodeling and histone- deacetylase multiprotein complex (NuRD). SUBCELLULAR LOCATION: Nucleus. TISSUE SPECIFICITY: No expression in nonepithelial cells. INDUCTION: By estrogen. SIMILARITY: Contains 1 BAH domain. SIMILARITY: Contains 1 ELM2 domain. SIMILARITY: Contains 1 GATA-type zinc finger. SIMILARITY: Contains 1 SANT domain. SEQUENCE CAUTION: Sequence=BAA86580.1; Type=Erroneous initiation;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: MTA3 Diseases sorted by gene-association score: gastroesophageal junction adenocarcinoma (16)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C023514 2,6-dinitrotoluene D014635 Valproic Acid D016604 Aflatoxin B1 D001564 Benzo(a)pyrene D019256 Cadmium Chloride D002995 Clofibric Acid D004026 Dieldrin D004052 Diethylnitrosamine D004958 Estradiol D006830 Hydralazine more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 13.19 RPKM in Adrenal Gland Total median expression: 310.70 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-59.40	114	-0.521	Picture	PostScript	Text
3' UTR	-1400.50	3547	-0.395	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR001025 - BAH_dom
IPR000949 - ELM2_dom
IPR009057 - Homeodomain-like
IPR001005 - SANT/Myb
IPR017884 - SANT_dom
IPR000679 - Znf_GATA

Pfam Domains:
PF00249 - Myb-like DNA-binding domain
PF00320 - GATA zinc finger
PF01426 - BAH domain
PF01448 - ELM2 domain
PF17226 - MTA R1 domain

SCOP Domains:
46689 - Homeodomain-like
82061 - BAH domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

ModBase Predicted Comparative 3D Structure on Q9BTC8


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	No ortholog
Gene Details	Gene Details		Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase
				Protein Sequence
				Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding GO:0003677 DNA binding GO:0003682 chromatin binding GO:0003700 transcription factor activity, sequence-specific DNA binding GO:0004407 histone deacetylase activity GO:0005515 protein binding GO:0008270 zinc ion binding GO:0043565 sequence-specific DNA binding GO:0044877 macromolecular complex binding GO:0046872 metal ion binding Biological Process: GO:0006355 regulation of transcription, DNA-templated GO:0006357 regulation of transcription from RNA polymerase II promoter GO:0008284 positive regulation of cell proliferation GO:0010971 positive regulation of G2/M transition of mitotic cell cycle GO:0016575 histone deacetylation GO:0045892 negative regulation of transcription, DNA-templated Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005737 cytoplasm GO:0043231 intracellular membrane-bounded organelle

Descriptions from all associated GenBank mRNAs


	AK127245 - Homo sapiens cDNA FLJ45312 fis, clone BRHIP3005037, moderately similar to Metastasis-associated protein MTA1. AB033092 - Homo sapiens KIAA1266 mRNA for KIAA1266 protein. BC053631 - Homo sapiens metastasis associated 1 family, member 3, mRNA (cDNA clone MGC:61556 IMAGE:6472900), complete cds. BC004227 - Homo sapiens metastasis associated 1 family, member 3, mRNA (cDNA clone MGC:4778 IMAGE:3542706), complete cds. AK027304 - Homo sapiens cDNA FLJ14398 fis, clone HEMBA1003569, moderately similar to METASTASIS-ASSOCIATED PROTEIN MTA1. CU678620 - Synthetic construct Homo sapiens gateway clone IMAGE:100017684 5' read MTA3 mRNA. AB384163 - Synthetic construct DNA, clone: pF1KSDA1266, Homo sapiens MTA3 gene for metastasis-associated protein MTA3, complete cds, without stop codon, in Flexi system. JD555486 - Sequence 536510 from Patent EP1572962. AF086450 - Homo sapiens full length insert cDNA clone ZD82D06. AK122690 - Homo sapiens cDNA FLJ16152 fis, clone BRAMY2047280, moderately similar to METASTASIS-ASSOCIATED PROTEIN MTA1. AL161954 - Homo sapiens mRNA; cDNA DKFZp434C2316 (from clone DKFZp434C2316); partial cds. JD134498 - Sequence 115522 from Patent EP1572962. JD335639 - Sequence 316663 from Patent EP1572962. JD450228 - Sequence 431252 from Patent EP1572962. JD291367 - Sequence 272391 from Patent EP1572962. JD372364 - Sequence 353388 from Patent EP1572962. JD331474 - Sequence 312498 from Patent EP1572962. JD249319 - Sequence 230343 from Patent EP1572962. JD486965 - Sequence 467989 from Patent EP1572962. JD196605 - Sequence 177629 from Patent EP1572962. JD549803 - Sequence 530827 from Patent EP1572962. JD292693 - Sequence 273717 from Patent EP1572962. JD269969 - Sequence 250993 from Patent EP1572962. JD299275 - Sequence 280299 from Patent EP1572962. JD528249 - Sequence 509273 from Patent EP1572962. JD565553 - Sequence 546577 from Patent EP1572962. JD210405 - Sequence 191429 from Patent EP1572962. JD125948 - Sequence 106972 from Patent EP1572962. JD483840 - Sequence 464864 from Patent EP1572962. JD198707 - Sequence 179731 from Patent EP1572962. JD351130 - Sequence 332154 from Patent EP1572962. JD095609 - Sequence 76633 from Patent EP1572962. JD157498 - Sequence 138522 from Patent EP1572962. JD525340 - Sequence 506364 from Patent EP1572962. JD286098 - Sequence 267122 from Patent EP1572962. JD334219 - Sequence 315243 from Patent EP1572962. JD065200 - Sequence 46224 from Patent EP1572962. JD155565 - Sequence 136589 from Patent EP1572962. JD294591 - Sequence 275615 from Patent EP1572962. JD359062 - Sequence 340086 from Patent EP1572962. JD175326 - Sequence 156350 from Patent EP1572962. JD446737 - Sequence 427761 from Patent EP1572962. JD521336 - Sequence 502360 from Patent EP1572962. JD386670 - Sequence 367694 from Patent EP1572962. JD317816 - Sequence 298840 from Patent EP1572962. JD167732 - Sequence 148756 from Patent EP1572962. JD553633 - Sequence 534657 from Patent EP1572962. JD434244 - Sequence 415268 from Patent EP1572962. JD157424 - Sequence 138448 from Patent EP1572962. JD371816 - Sequence 352840 from Patent EP1572962. JD117859 - Sequence 98883 from Patent EP1572962. JD107090 - Sequence 88114 from Patent EP1572962. JD096167 - Sequence 77191 from Patent EP1572962. JD184466 - Sequence 165490 from Patent EP1572962. JD565420 - Sequence 546444 from Patent EP1572962. JD530254 - Sequence 511278 from Patent EP1572962. JD342696 - Sequence 323720 from Patent EP1572962. JD086357 - Sequence 67381 from Patent EP1572962. JD179928 - Sequence 160952 from Patent EP1572962. JD492349 - Sequence 473373 from Patent EP1572962. JD539917 - Sequence 520941 from Patent EP1572962. JD391107 - Sequence 372131 from Patent EP1572962. JD318274 - Sequence 299298 from Patent EP1572962. JD156366 - Sequence 137390 from Patent EP1572962. JD461031 - Sequence 442055 from Patent EP1572962. JD139657 - Sequence 120681 from Patent EP1572962. JD105449 - Sequence 86473 from Patent EP1572962. JD376858 - Sequence 357882 from Patent EP1572962. JD445887 - Sequence 426911 from Patent EP1572962. JD214326 - Sequence 195350 from Patent EP1572962. JD122577 - Sequence 103601 from Patent EP1572962. JD216221 - Sequence 197245 from Patent EP1572962. JD268386 - Sequence 249410 from Patent EP1572962. JD297638 - Sequence 278662 from Patent EP1572962. JD216575 - Sequence 197599 from Patent EP1572962. JD383798 - Sequence 364822 from Patent EP1572962. JD234482 - Sequence 215506 from Patent EP1572962. JD099241 - Sequence 80265 from Patent EP1572962. JD390868 - Sequence 371892 from Patent EP1572962. JD177208 - Sequence 158232 from Patent EP1572962. JD109097 - Sequence 90121 from Patent EP1572962. JD443788 - Sequence 424812 from Patent EP1572962. JD296436 - Sequence 277460 from Patent EP1572962. JD488791 - Sequence 469815 from Patent EP1572962. JD551108 - Sequence 532132 from Patent EP1572962. JD565727 - Sequence 546751 from Patent EP1572962. JD485277 - Sequence 466301 from Patent EP1572962. JD061382 - Sequence 42406 from Patent EP1572962. JD109865 - Sequence 90889 from Patent EP1572962. JD233162 - Sequence 214186 from Patent EP1572962.

Biochemical and Signaling Pathways


	BioCarta from NCI Cancer Genome Anatomy Project h_mta3Pathway - Downregulated of MTA-3 in ER-negative Breast Tumors Reactome (by CSHL, EBI, and GO) Protein Q9BTC8 (Reactome details) participates in the following event(s): R-HSA-427404 Recruitment of ERCC6 (CSB), EHMT2 (G9a), and NuRD to the promoter of rRNA gene R-HSA-8943780 SALL4 recruits NuRD to PTEN gene R-HSA-427336 TTF1:rRNA promoter:ERCC6:EHMT2 complex dimethylates histone H3 at lysine-9. R-HSA-3769447 HDAC1/2 containing-complexes deacetylate histones R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression R-HSA-8943724 Regulation of PTEN gene transcription R-HSA-5250913 Positive epigenetic regulation of rRNA expression R-HSA-6807070 PTEN Regulation R-HSA-3214815 HDACs deacetylate histones R-HSA-212165 Epigenetic regulation of gene expression R-HSA-1257604 PIP3 activates AKT signaling R-HSA-3247509 Chromatin modifying enzymes R-HSA-74160 Gene expression (Transcription) R-HSA-9006925 Intracellular signaling by second messengers R-HSA-4839726 Chromatin organization R-HSA-162582 Signal Transduction

Other Names for This Gene


	Alternate Gene Symbols: ENST00000405094.1, KIAA1266, MTA3_HUMAN, NM_001330444, Q9BTC8, Q9NSP2, Q9ULF4, uc319cxa.1, uc319cxa.2 UCSC ID: ENST00000405094.2_12 RefSeq Accession: NM_001330442.2 Protein: Q9BTC8 (aka MTA3_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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