Human Gene RPH3A (ENST00000389385.9_7) from GENCODE V47lift37

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Description: rabphilin 3A, transcript variant 8 (from RefSeq NR_145127.2)
Gencode Transcript: ENST00000389385.9_7
Gencode Gene: ENSG00000089169.15_15
Transcript (Including UTRs)
Position: hg19 chr12:113,229,553-113,336,686 Size: 107,134 Total Exon Count: 22 Strand: +
Coding Region
Position: hg19 chr12:113,266,124-113,334,585 Size: 68,462 Coding Exon Count: 20

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	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 (chr12:113,229,553-113,336,686)			mRNA (may differ from genome)		Protein (694 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	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: RP3A_HUMAN DESCRIPTION: RecName: Full=Rabphilin-3A; AltName: Full=Exophilin-1; FUNCTION: Protein transport. Probably involved with Ras-related protein Rab-3A in synaptic vesicle traffic and/or synaptic vesicle fusion. Could play a role in neurotransmitter release by regulating membrane flow in the nerve terminal (By similarity). INTERACTION: O14936:CASK; NbExp=3; IntAct=EBI-1216802, EBI-1215506; SUBCELLULAR LOCATION: Cell junction, synapse (By similarity). SIMILARITY: Contains 2 C2 domains. SIMILARITY: Contains 1 FYVE-type zinc finger. SIMILARITY: Contains 1 RabBD (Rab-binding) domain. SEQUENCE CAUTION: Sequence=BAA76829.2; 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: RPH3A Diseases sorted by gene-association score: infundibulo-neurohypophysitis (8), synucleinopathy (2)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone D000643 Ammonium Chloride D001205 Ascorbic Acid D004052 Diethylnitrosamine D000431 Ethanol D019833 Genistein D009020 Morphine D018817 N-Methyl-3,4-methylenedioxyamphetamine D009538 Nicotine D013759 Tetrahydrocannabinol more ... click here to view the complete list

Common Gene Haplotype Alleles


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

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


	Highest median expression: 47.54 RPKM in Brain - Frontal Cortex (BA9) Total median expression: 258.71 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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-137.30	404	-0.340	Picture	PostScript	Text
3' UTR	-554.50	2101	-0.264	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
IPR000008 - C2_Ca-dep
IPR008973 - C2_Ca/lipid-bd_dom_CaLB
IPR020477 - C2_dom
IPR018029 - C2_membr_targeting
IPR010911 - Rab-bd_domain
IPR003315 - Rabphilin3A_effector_Zn-bd
IPR001565 - Synaptotagmin
IPR017455 - Znf_FYVE-rel
IPR011011 - Znf_FYVE_PHD
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00168 - C2 domain
PF02318 - FYVE-type zinc finger

SCOP Domains:
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
57889 - Cysteine-rich domain
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q9Y2J0


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	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0005509 calcium ion binding GO:0005515 protein binding GO:0005544 calcium-dependent phospholipid binding GO:0005546 phosphatidylinositol-4,5-bisphosphate binding GO:0008270 zinc ion binding GO:0008289 lipid binding GO:0008430 selenium binding GO:0017137 Rab GTPase binding GO:0019905 syntaxin binding GO:0030276 clathrin binding GO:0042301 phosphate ion binding GO:0044877 macromolecular complex binding GO:0046872 metal ion binding GO:0070679 inositol 1,4,5 trisphosphate binding GO:1901981 phosphatidylinositol phosphate binding Biological Process: GO:0006886 intracellular protein transport GO:0006906 vesicle fusion GO:0015031 protein transport GO:0017158 regulation of calcium ion-dependent exocytosis GO:0048791 calcium ion-regulated exocytosis of neurotransmitter Cellular Component: GO:0005829 cytosol GO:0005886 plasma membrane GO:0008021 synaptic vesicle GO:0016020 membrane GO:0019898 extrinsic component of membrane GO:0030054 cell junction GO:0030141 secretory granule GO:0030672 synaptic vesicle membrane GO:0032991 macromolecular complex GO:0043005 neuron projection GO:0045202 synapse GO:0005794 Golgi apparatus

Descriptions from all associated GenBank mRNAs


	AK295696 - Homo sapiens cDNA FLJ58761 complete cds, highly similar to Rabphilin-3A. AB023202 - Homo sapiens KIAA0985 mRNA for KIAA0985 protein. AK316112 - Homo sapiens cDNA, FLJ79011 complete cds, highly similar to Rabphilin-3A. BC017259 - Homo sapiens rabphilin 3A homolog (mouse), mRNA (cDNA clone MGC:29559 IMAGE:3510158), complete cds. BC002605 - Homo sapiens rabphilin 3A homolog (mouse), mRNA (cDNA clone IMAGE:3160482), partial cds. AK296296 - Homo sapiens cDNA FLJ52312 complete cds, highly similar to Rabphilin-3A. BC009843 - Homo sapiens rabphilin 3A homolog (mouse), mRNA (cDNA clone IMAGE:3944479), partial cds. JD111402 - Sequence 92426 from Patent EP1572962. JD090508 - Sequence 71532 from Patent EP1572962. JD526742 - Sequence 507766 from Patent EP1572962. JD055109 - Sequence 36133 from Patent EP1572962. CU677889 - Synthetic construct Homo sapiens gateway clone IMAGE:100020019 5' read RPH3A mRNA. AB385413 - Synthetic construct DNA, clone: pF1KA0985, Homo sapiens RPH3A gene for rabphilin-3A, complete cds, without stop codon, in Flexi system. KJ898418 - Synthetic construct Homo sapiens clone ccsbBroadEn_07812 RPH3A gene, encodes complete protein. BX647281 - Homo sapiens mRNA; cDNA DKFZp686N1588 (from clone DKFZp686N1588). JD387640 - Sequence 368664 from Patent EP1572962. JD399864 - Sequence 380888 from Patent EP1572962. JD360779 - Sequence 341803 from Patent EP1572962. JD356116 - Sequence 337140 from Patent EP1572962. JD439802 - Sequence 420826 from Patent EP1572962. JD354793 - Sequence 335817 from Patent EP1572962. JD060016 - Sequence 41040 from Patent EP1572962. JD499989 - Sequence 481013 from Patent EP1572962. JD055555 - Sequence 36579 from Patent EP1572962. JD527576 - Sequence 508600 from Patent EP1572962. JD242967 - Sequence 223991 from Patent EP1572962. JD524640 - Sequence 505664 from Patent EP1572962. JD514191 - Sequence 495215 from Patent EP1572962. JD392136 - Sequence 373160 from Patent EP1572962. JD519709 - Sequence 500733 from Patent EP1572962. JD130650 - Sequence 111674 from Patent EP1572962. JD439226 - Sequence 420250 from Patent EP1572962. JD310337 - Sequence 291361 from Patent EP1572962. JD459879 - Sequence 440903 from Patent EP1572962. JD149515 - Sequence 130539 from Patent EP1572962. JD525703 - Sequence 506727 from Patent EP1572962. JD154582 - Sequence 135606 from Patent EP1572962. JD324315 - Sequence 305339 from Patent EP1572962. JD257863 - Sequence 238887 from Patent EP1572962. JD203231 - Sequence 184255 from Patent EP1572962. JD441171 - Sequence 422195 from Patent EP1572962. JD064027 - Sequence 45051 from Patent EP1572962. JD248940 - Sequence 229964 from Patent EP1572962. JD434114 - Sequence 415138 from Patent EP1572962. JD240710 - Sequence 221734 from Patent EP1572962. JD307454 - Sequence 288478 from Patent EP1572962. JD516405 - Sequence 497429 from Patent EP1572962. JD134583 - Sequence 115607 from Patent EP1572962. JD339309 - Sequence 320333 from Patent EP1572962. JD381176 - Sequence 362200 from Patent EP1572962. JD222759 - Sequence 203783 from Patent EP1572962. JD200976 - Sequence 182000 from Patent EP1572962. JD248715 - Sequence 229739 from Patent EP1572962. JD535252 - Sequence 516276 from Patent EP1572962. JD270798 - Sequence 251822 from Patent EP1572962. JD305566 - Sequence 286590 from Patent EP1572962. JD101013 - Sequence 82037 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: B7Z3C3, ENST00000389385.1, ENST00000389385.2, ENST00000389385.3, ENST00000389385.4, ENST00000389385.5, ENST00000389385.6, ENST00000389385.7, ENST00000389385.8, KIAA0985, NR_145127, Q96AE0, Q9Y2J0, RP3A_HUMAN, uc318tet.1, uc318tet.2 UCSC ID: ENST00000389385.9_7 RefSeq Accession: NM_001143854.2 Protein: Q9Y2J0 (aka RP3A_HUMAN)

Gene Model Information


	Click here for a detailed description of the fields of the table above.

Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.