Human Gene APOBEC3D (ENST00000216099.13) from GENCODE V44
  Description: Homo sapiens apolipoprotein B mRNA editing enzyme catalytic subunit 3D (APOBEC3D), transcript variant 1, mRNA. (from RefSeq NM_152426)
RefSeq Summary (NM_152426): This gene is a member of the cytidine deaminase gene family. It is one of a group of related genes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1 and inhibit retroviruses, such as HIV, by deaminating cytosine residues in nascent retroviral cDNA. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENST00000216099.13
Gencode Gene: ENSG00000243811.12
Transcript (Including UTRs)
   Position: hg38 chr22:39,021,127-39,033,277 Size: 12,151 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg38 chr22:39,021,520-39,032,316 Size: 10,797 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:39,021,127-39,033,277)mRNA (may differ from genome)Protein (386 aa)
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OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ABC3D_HUMAN
DESCRIPTION: RecName: Full=Probable DNA dC->dU-editing enzyme APOBEC-3D; EC=3.5.4.-;
FUNCTION: Probable DNA cytidine deaminase involved in foreign DNA clearance. May provide cellular innate resistance to a specific panel of genetic invaders including endogenous retroelements and a subset of viruses.
CATALYTIC ACTIVITY: Cytidine + H(2)O = uridine + NH(3).
COFACTOR: Zinc (By similarity).
TISSUE SPECIFICITY: Expressed in lymphoid organs. Also detected in non-lymphoid tissues including lung.
MISCELLANEOUS: It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22.
SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase family.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.64 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 75.45 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -144.10393-0.367 Picture PostScript Text
3' UTR -368.10961-0.383 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
IPR016192 - APOBEC/CMP_deaminase_Zn-bd
IPR007904 - APOBEC_C
IPR016193 - Cytidine_deaminase-like

Pfam Domains:
PF05240 - APOBEC-like C-terminal domain

ModBase Predicted Comparative 3D Structure on Q96AK3
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
GO:0046872 metal ion binding

Biological Process:
GO:0002376 immune system process
GO:0010529 negative regulation of transposition
GO:0045087 innate immune response
GO:0045869 negative regulation of single stranded viral RNA replication via double stranded DNA intermediate
GO:0051607 defense response to virus
GO:0070383 DNA cytosine deamination

Cellular Component:
GO:0000932 P-body
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK094570 - Homo sapiens cDNA FLJ37251 fis, clone BRAMY2007043, highly similar to Homo sapiens phorbolin I protein (PBI) mRNA.
BC082754 - Homo sapiens cDNA clone IMAGE:5483925, **** WARNING: chimeric clone ****.
CR456396 - Homo sapiens bK150C2.9 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.bK150C2.9).
BC017022 - Homo sapiens apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D, mRNA (cDNA clone IMAGE:3915193), **** WARNING: chimeric clone ****.
JD065912 - Sequence 46936 from Patent EP1572962.
JD065913 - Sequence 46937 from Patent EP1572962.
AB528855 - Synthetic construct DNA, clone: pF1KE0576, Homo sapiens APOBEC3D gene for apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D, without stop codon, in Flexi system.
BC148619 - Synthetic construct Homo sapiens clone IMAGE:100015580, MGC:183104 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (APOBEC3D) mRNA, encodes complete protein.
BC153185 - Synthetic construct Homo sapiens clone IMAGE:100016554, MGC:184326 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (APOBEC3D) mRNA, encodes complete protein.
AB527109 - Synthetic construct DNA, clone: pF1KB3445, Homo sapiens APOBEC3D gene for apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D, without stop codon, in Flexi system.
CU013242 - Homo sapiens APOBEC3D, mRNA (cDNA clone IMAGE:100000021), complete cds, without stop codon, in Gateway system.
KJ900194 - Synthetic construct Homo sapiens clone ccsbBroadEn_09588 APOBEC3D gene, encodes complete protein.
CU012954 - Homo sapiens APOBEC3D, mRNA (cDNA clone IMAGE:100000117), complete cds, with stop codon, in Gateway system.
EU527884 - Homo sapiens apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3DE (APOBEC3DE) mRNA, complete cds.
DQ578379 - Homo sapiens piRNA piR-46491, complete sequence.
JD070616 - Sequence 51640 from Patent EP1572962.
JD217026 - Sequence 198050 from Patent EP1572962.
JD426991 - Sequence 408015 from Patent EP1572962.
JD254853 - Sequence 235877 from Patent EP1572962.
JD255568 - Sequence 236592 from Patent EP1572962.
JD527714 - Sequence 508738 from Patent EP1572962.
JD161530 - Sequence 142554 from Patent EP1572962.
JD161531 - Sequence 142555 from Patent EP1572962.
JD547604 - Sequence 528628 from Patent EP1572962.
JD547605 - Sequence 528629 from Patent EP1572962.
JD227584 - Sequence 208608 from Patent EP1572962.
JD227585 - Sequence 208609 from Patent EP1572962.
JD456808 - Sequence 437832 from Patent EP1572962.
JD456809 - Sequence 437833 from Patent EP1572962.
JD386935 - Sequence 367959 from Patent EP1572962.
JD543795 - Sequence 524819 from Patent EP1572962.
JD345567 - Sequence 326591 from Patent EP1572962.
JD242997 - Sequence 224021 from Patent EP1572962.
JD213656 - Sequence 194680 from Patent EP1572962.
JD163470 - Sequence 144494 from Patent EP1572962.
JD554470 - Sequence 535494 from Patent EP1572962.
JD379737 - Sequence 360761 from Patent EP1572962.
JD094151 - Sequence 75175 from Patent EP1572962.
JD312190 - Sequence 293214 from Patent EP1572962.
JD346672 - Sequence 327696 from Patent EP1572962.
JD346673 - Sequence 327697 from Patent EP1572962.
JD136347 - Sequence 117371 from Patent EP1572962.
JD136348 - Sequence 117372 from Patent EP1572962.
JD251320 - Sequence 232344 from Patent EP1572962.
JD109769 - Sequence 90793 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ABC3D_HUMAN, ENST00000216099.1, ENST00000216099.10, ENST00000216099.11, ENST00000216099.12, ENST00000216099.2, ENST00000216099.3, ENST00000216099.4, ENST00000216099.5, ENST00000216099.6, ENST00000216099.7, ENST00000216099.8, ENST00000216099.9, NM_152426, Q5JZ91, Q7Z2N2, Q7Z2N5, Q7Z2N6, Q96AK3, uc003awt.1, uc003awt.2, uc003awt.3, uc003awt.4, uc003awt.5, uc003awt.6
UCSC ID: ENST00000216099.13
RefSeq Accession: NM_152426
Protein: Q96AK3 (aka ABC3D_HUMAN or AC3D_HUMAN)
CCDS: CCDS46709.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.