EuRBPDB

Basic Information
Cancer Related Information

Description

RBDs

RBPome

Expression

Transcripts

Gene Model

Pathways

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000243811 (Gene tree)
Gene ID: 140564
Gene Symbol: APOBEC3D
Alias: ARP6|APOBEC3DE|APOBEC3E
Full Name: apolipoprotein B mRNA editing enzyme catalytic subunit 3D
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 12,164 bases
Position: chr22:39,021,113-39,033,276
Accession: 17354
RBP type: canonical RBP
Summary: 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]

RNA binding domains(RBDs)

Protein ID	Domain	Pfam ID	E-value	Domain number	Total number
ENSP00000216099	APOBEC_N	PF08210.11	6.2e-98	1	2
ENSP00000216099	APOBEC_N	PF08210.11	6.2e-98	2	2
ENSP00000480718	APOBEC_N	PF08210.11	6.7e-54	1	1
ENSP00000388017	APOBEC_N	PF08210.11	8.5e-50	1	1
ENSP00000216099	APOBEC_C	PF05240.14	1.2e-60	1	2
ENSP00000216099	APOBEC_C	PF05240.14	1.2e-60	2	2
ENSP00000480718	APOBEC_C	PF05240.14	4.5e-31	1	1
ENSP00000388017	APOBEC_C	PF05240.14	5.3e-31	1	1

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30352994	Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture	RIC & Jurkat	2018 Oct 23	Perez-Perri JI	DOI:10.1038/s41467-018-06557-8

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000622217	APOBEC3D-203	591	-	ENSP00000480718	190 (aa)	-	A0A087WX48
ENST00000216099	APOBEC3D-201	2528	XM_017028596	ENSP00000216099	386 (aa)	XP_016884085	Q96AK3
ENST00000427494	APOBEC3D-202	1961	XM_005261337	ENSP00000388017	202 (aa)	XP_005261394	Q6ICH2

Gene Model

Click here to download ENSG00000243811's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa05170	Human immunodeficiency virus 1 infection	KEGG

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000243811's network

* RBP PPI network refers to all genes directly bind to RBP

Orthologs

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000243811	APOBEC3D	100	68.947	ENSANAG00000030088	-	99	67.358	Aotus_nancymaae
ENSG00000243811	APOBEC3D	69	68.182	ENSCJAG00000015317	-	100	68.182	Callithrix_jacchus
ENSG00000243811	APOBEC3D	99	47.594	ENSCAFG00020002615	-	99	47.594	Canis_lupus_dingo
ENSG00000243811	APOBEC3D	97	51.913	ENSTSYG00000028254	-	99	51.913	Carlito_syrichta
ENSG00000243811	APOBEC3D	100	51.323	ENSTSYG00000034260	-	97	51.323	Carlito_syrichta
ENSG00000243811	APOBEC3D	98	48.634	ENSTSYG00000030036	-	99	48.634	Carlito_syrichta
ENSG00000243811	APOBEC3D	98	66.129	ENSCCAG00000030932	-	90	63.000	Cebus_capucinus
ENSG00000243811	APOBEC3D	98	76.630	ENSCATG00000033502	-	100	74.731	Cercocebus_atys
ENSG00000243811	APOBEC3D	100	72.632	ENSCATG00000043226	APOBEC3C	100	72.632	Cercocebus_atys
ENSG00000243811	APOBEC3D	100	72.632	ENSCSAG00000006402	APOBEC3C	100	72.632	Chlorocebus_sabaeus
ENSG00000243811	APOBEC3D	100	78.495	ENSCSAG00000006382	APOBEC3F	100	78.495	Chlorocebus_sabaeus
ENSG00000243811	APOBEC3D	100	76.344	ENSCANG00000033269	-	99	78.261	Colobus_angolensis_palliatus
ENSG00000243811	APOBEC3D	100	73.684	ENSCANG00000039177	APOBEC3C	100	73.684	Colobus_angolensis_palliatus
ENSG00000243811	APOBEC3D	100	78.495	ENSCANG00000032904	-	100	78.495	Colobus_angolensis_palliatus
ENSG00000243811	APOBEC3D	100	75.806	ENSCANG00000031957	-	100	75.806	Colobus_angolensis_palliatus
ENSG00000243811	APOBEC3D	97	38.830	ENSDNOG00000044642	-	99	38.830	Dasypus_novemcinctus
ENSG00000243811	APOBEC3D	100	46.341	ENSEASG00005018641	-	100	46.341	Equus_asinus_asinus
ENSG00000243811	APOBEC3D	99	47.027	ENSECAG00000006071	-	100	46.237	Equus_caballus
ENSG00000243811	APOBEC3D	100	88.421	ENSGGOG00000036587	-	100	88.421	Gorilla_gorilla
ENSG00000243811	APOBEC3D	100	87.097	ENSGGOG00000038678	APOBEC3F	100	87.097	Gorilla_gorilla
ENSG00000243811	APOBEC3D	98	45.213	ENSHGLG00000017315	-	91	42.119	Heterocephalus_glaber_female
ENSG00000243811	APOBEC3D	98	45.213	ENSHGLG00100003105	-	94	45.213	Heterocephalus_glaber_male
ENSG00000243811	APOBEC3D	100	76.882	ENSMFAG00000002331	-	100	76.882	Macaca_fascicularis
ENSG00000243811	APOBEC3D	100	73.158	ENSMFAG00000016792	APOBEC3C	100	73.158	Macaca_fascicularis
ENSG00000243811	APOBEC3D	100	75.806	ENSMFAG00000004037	APOBEC3F	100	75.806	Macaca_fascicularis
ENSG00000243811	APOBEC3D	99	72.432	ENSMMUG00000004018	APOBEC3C	95	72.826	Macaca_mulatta
ENSG00000243811	APOBEC3D	100	77.419	ENSMMUG00000004017	APOBEC3F	100	77.419	Macaca_mulatta
ENSG00000243811	APOBEC3D	100	73.684	ENSMNEG00000045196	APOBEC3C	100	73.684	Macaca_nemestrina
ENSG00000243811	APOBEC3D	100	77.215	ENSMNEG00000043316	APOBEC3D	100	77.215	Macaca_nemestrina
ENSG00000243811	APOBEC3D	100	73.158	ENSMLEG00000036992	APOBEC3C	100	73.158	Mandrillus_leucophaeus
ENSG00000243811	APOBEC3D	100	77.957	ENSMLEG00000029642	APOBEC3F	100	77.957	Mandrillus_leucophaeus
ENSG00000243811	APOBEC3D	99	52.128	ENSMICG00000042615	-	89	52.128	Microcebus_murinus
ENSG00000243811	APOBEC3D	97	44.503	ENSMLUG00000023676	-	99	44.503	Myotis_lucifugus
ENSG00000243811	APOBEC3D	100	77.720	ENSNLEG00000035811	-	100	77.720	Nomascus_leucogenys
ENSG00000243811	APOBEC3D	100	74.211	ENSNLEG00000028392	APOBEC3C	100	74.211	Nomascus_leucogenys
ENSG00000243811	APOBEC3D	98	44.134	ENSOGAG00000033404	-	100	44.134	Otolemur_garnettii
ENSG00000243811	APOBEC3D	99	43.284	ENSOGAG00000030300	-	99	42.553	Otolemur_garnettii
ENSG00000243811	APOBEC3D	98	47.312	ENSOGAG00000032498	-	99	47.312	Otolemur_garnettii
ENSG00000243811	APOBEC3D	100	90.526	ENSPPAG00000028218	-	100	90.526	Pan_paniscus
ENSG00000243811	APOBEC3D	100	78.947	ENSPPAG00000014118	APOBEC3C	100	78.947	Pan_paniscus
ENSG00000243811	APOBEC3D	99	47.027	ENSPPRG00000003726	-	98	47.027	Panthera_pardus
ENSG00000243811	APOBEC3D	100	92.079	ENSPTRG00000041588	APOBEC3D	100	92.079	Pan_troglodytes
ENSG00000243811	APOBEC3D	100	87.097	ENSPTRG00000014385	APOBEC3C	100	87.097	Pan_troglodytes
ENSG00000243811	APOBEC3D	100	76.344	ENSPANG00000010775	APOBEC3F	100	76.344	Papio_anubis
ENSG00000243811	APOBEC3D	100	77.368	ENSPPYG00000011832	APOBEC3C	100	77.368	Pongo_abelii
ENSG00000243811	APOBEC3D	68	53.488	ENSPCOG00000022067	-	98	53.488	Propithecus_coquereli
ENSG00000243811	APOBEC3D	66	54.762	ENSPCOG00000018072	-	95	54.762	Propithecus_coquereli
ENSG00000243811	APOBEC3D	94	44.715	ENSPVAG00000009461	-	71	44.715	Pteropus_vampyrus
ENSG00000243811	APOBEC3D	98	79.570	ENSRBIG00000030323	-	100	79.570	Rhinopithecus_bieti
ENSG00000243811	APOBEC3D	100	78.261	ENSRBIG00000030834	-	100	78.261	Rhinopithecus_bieti
ENSG00000243811	APOBEC3D	100	77.778	ENSRBIG00000042297	-	100	77.778	Rhinopithecus_bieti
ENSG00000243811	APOBEC3D	100	77.778	ENSRROG00000029996	-	100	77.778	Rhinopithecus_roxellana
ENSG00000243811	APOBEC3D	100	77.419	ENSRROG00000029045	APOBEC3C	100	77.419	Rhinopithecus_roxellana
ENSG00000243811	APOBEC3D	100	77.717	ENSRROG00000028557	-	100	77.717	Rhinopithecus_roxellana
ENSG00000243811	APOBEC3D	100	68.421	ENSSBOG00000032780	-	100	68.421	Saimiri_boliviensis_boliviensis
ENSG00000243811	APOBEC3D	96	43.407	ENSUAMG00000004433	-	100	43.407	Ursus_americanus
ENSG00000243811	APOBEC3D	97	44.324	ENSUMAG00000014441	-	86	44.324	Ursus_maritimus
ENSG00000243811	APOBEC3D	79	51.007	ENSVVUG00000014628	-	94	50.746	Vulpes_vulpes

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000932	P-body	21873635.	IBA	Component
GO:0000932	P-body	22915799.	IDA	Component
GO:0003723	RNA binding	21873635.	IBA	Function
GO:0004126	cytidine deaminase activity	21873635.	IBA	Function
GO:0005634	nucleus	21873635.	IBA	Component
GO:0005737	cytoplasm	21873635.	IBA	Component
GO:0005737	cytoplasm	21835787.	IDA	Component
GO:0008270	zinc ion binding	-	IEA	Function
GO:0009972	cytidine deamination	-	IEA	Process
GO:0010529	negative regulation of transposition	21873635.	IBA	Process
GO:0010529	negative regulation of transposition	20062055.	IDA	Process
GO:0016554	cytidine to uridine editing	21873635.	IBA	Process
GO:0045087	innate immune response	-	IEA	Process
GO:0045869	negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	21873635.	IBA	Process
GO:0045869	negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	21835787.	IDA	Process
GO:0051607	defense response to virus	21873635.	IBA	Process
GO:0051607	defense response to virus	21835787.	IDA	Process
GO:0070383	DNA cytosine deamination	21873635.	IBA	Process
GO:0070383	DNA cytosine deamination	21835787.	IDA	Process
GO:0080111	DNA demethylation	21873635.	IBA	Process

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq	RBD
BLCA	chr22	39029369	Silent	rs779214802	P204P	0.32
BLCA	chr22	39025085	Missense_Mutation	rs773998723	E76K	0.27
BLCA	chr22	39029459	Silent	novel	T234T	0.28
BLCA	chr22	39025554	Splice_Region	novel		0.27
BLCA	chr22	39032278	Nonsense_Mutation	rs765057107	R375*	0.48
BLCA	chr22	39021492	5'UTR	novel		0.25
BRCA	chr22	39032247	Silent	rs201378161	F364F	0.24
BRCA	chr22	39022873	Silent	rs780066160	N23N	0.34
CESC	chr22	39025624	Silent	rs755076267	F186F	0.3
CESC	chr22	39021534	Splice_Region	NA	I5I	0.21
CESC	chr22	39031897	Silent	NA	F322F	0.4
CESC	chr22	39025554	Splice_Region	novel		0.37
CHOL	chr22	39032401	3'UTR	novel		0.5
COAD	chr22	39025227	Missense_Mutation	NA	H123L	0.45
COAD	chr22	39031783	Silent	NA	V284V	0.35
COAD	chr22	39029409	Missense_Mutation	NA	K218E	0.36
COAD	chr22	39022978	Silent	rs781113384	P58P	0.34
COAD	chr22	39021475	5'UTR	rs760595347		0.41
COAD	chr22	39025180	Frame_Shift_Del	NA	*C109Afs6**	0.35
COAD	chr22	39021458	5'UTR	NA		0.48
COAD	chr22	39022878	Missense_Mutation	novel	P25H	0.17
COAD	chr22	39032366	3'UTR	rs759513202		0.33
DLBC	chr22	39025638	Missense_Mutation	novel	A191V	0.42	APOBEC_N
ESCA	chr22	39032326	3'UTR	novel		0.13
ESCA	chr22	39025255	Silent	rs368364402	A132A	0.41
GBM	chr22	39032329	3'UTR	novel		0.09
HNSC	chr22	39021460	5'UTR	novel		0.24
HNSC	chr22	39032452	3'UTR	novel		0.23
HNSC	chr22	39025327	Silent	rs371920813	R156R	0.47
HNSC	chr22	39031868	Missense_Mutation	novel	T313A	0.17
HNSC	chr22	39029396	Missense_Mutation	novel	F213L	0.19
KIRC	chr22	39029417	Silent	NA	L220L	0.52
LGG	chr22	39025193	Missense_Mutation	novel	C112R	0.12
LGG	chr22	39025569	Missense_Mutation	novel	C168Y	0.08	APOBEC_N
LGG	chr22	39029369	Silent	rs779214802	P204P	0.25
LIHC	chr22	39025636	Silent	NA	Y190Y	0.37
LIHC	chr22	39025145	Silent	NA	R96R	0.33
LUAD	chr22	39025319	Frame_Shift_Del	novel	*A155Pfs3**	0.18	APOBEC_N
LUAD	chr22	39029492	Silent	novel	F245F	0.12
LUAD	chr22	39032401	3'UTR	novel		0.39
LUAD	chr22	39032300	Missense_Mutation	novel	R382L	0.43
LUAD	chr22	39022925	Missense_Mutation	novel	I41L	0.22
LUAD	chr22	39025151	Missense_Mutation	NA	F98I	0.37
LUAD	chr22	39032326	3'UTR	novel		0.11
LUSC	chr22	39021428	5'UTR	novel		0.16
LUSC	chr22	39031721	Nonsense_Mutation	novel	E264*	0.26
LUSC	chr22	39031955	Missense_Mutation	rs376325106	K342E	0.22
OV	chr22	39031834	Silent	rs751024970	A301A	0.75
OV	chr22	39022937	Missense_Mutation	novel	R45S	0.07
OV	chr22	39021470	5'UTR	novel		0.08
OV	chr22	39031723	Missense_Mutation	novel	E264D	0.1
PAAD	chr22	39022959	Missense_Mutation	novel	T52I	0.17
PRAD	chr22	39032325	3'UTR	novel		0.23
PRAD	chr22	39025241	Silent	NA	L128L	0.07
READ	chr22	39025289	Missense_Mutation	rs749813878	R144W	0.28	APOBEC_N
SKCM	chr22	39031705	Silent	NA	E258E	0.21
SKCM	chr22	39022874	Missense_Mutation	rs746961335	E24K	0.34
SKCM	chr22	39022949	Missense_Mutation	NA	L49F	0.44
SKCM	chr22	39025078	Silent	NA	F73F	0.29
SKCM	chr22	39025078	Silent	NA	F73F	0.37
SKCM	chr22	39022877	Missense_Mutation	NA	P25A	0.33
SKCM	chr22	39025255	Silent	NA	A132A	0.26
SKCM	chr22	39031840	Silent	NA	F303F	0.11
SKCM	chr22	39029368	Missense_Mutation	rs757469920	P204L	0.44
SKCM	chr22	39025136	Missense_Mutation	NA	P93S	0.14
SKCM	chr22	39025251	Missense_Mutation	rs776446805	S131F	0.38	APOBEC_N
SKCM	chr22	39031951	Silent	rs763859536	S340S	0.51
STAD	chr22	39022978	Silent	rs781113384	P58P	0.24
STAD	chr22	39022937	Missense_Mutation	NA	R45C	0.15
STAD	chr22	39032454	3'UTR	novel		0.24
STAD	chr22	39025130	Nonsense_Mutation	NA	R91*	0.27
STAD	chr22	39022936	Silent	NA	G44G	0.17
UCEC	chr22	39022835	Missense_Mutation	novel	R11W	0.3
UCEC	chr22	39025316	Missense_Mutation	NA	A153T	0.41	APOBEC_N
UCEC	chr22	39025591	Silent	NA	N175N	0.39
UCEC	chr22	39025624	Silent	rs755076267	F186F	0.38
UCEC	chr22	39032454	3'UTR	novel		0.75
UCEC	chr22	39031757	Silent	NA	L276L	0.13
UCEC	chr22	39031883	Missense_Mutation	rs745893074	R318C	0.46
UCEC	chr22	39032371	3'UTR	rs769515335		0.43
UCEC	chr22	39025208	Missense_Mutation	NA	T117A	0.26
UCEC	chr22	39031880	Missense_Mutation	novel	A317T	0.22
UCEC	chr22	39021429	5'UTR	novel		0.43
UCEC	chr22	39025615	Nonsense_Mutation	NA	W183*	0.38	APOBEC_N
UCEC	chr22	39025624	Silent	rs755076267	F186F	0.39
UCEC	chr22	39032356	3'UTR	novel		0.14
UCEC	chr22	39032316	Nonstop_Mutation	novel	387Wext12	0.39
UCEC	chr22	39022960	Silent	novel	T52T	0.2
UCEC	chr22	39025186	Silent	novel	C109C	0.2
UCEC	chr22	39032278	Nonsense_Mutation	rs765057107	R375*	0.46
UCEC	chr22	39029485	Missense_Mutation	novel	A243D	0.29
UCEC	chr22	39025094	Missense_Mutation	novel	A79T	0.44
UCEC	chr22	39025149	Missense_Mutation	rs748680344	R97H	0.5
UCEC	chr22	39025624	Silent	rs755076267	F186F	0.49
UCEC	chr22	39025649	Missense_Mutation	rs746506547	R195C	0.47	APOBEC_N
UCEC	chr22	39032408	3'UTR	novel		0.3
UCEC	chr22	39032286	Silent	novel	L377L	0.21
UCEC	chr22	39022999	Silent	rs768017264	S65S	0.14
UCEC	chr22	39025169	Missense_Mutation	novel	V104I	0.44
UCEC	chr22	39025641	Missense_Mutation	novel	S192Y	0.38	APOBEC_N
UCEC	chr22	39025624	Silent	rs755076267	F186F	0.47
UCEC	chr22	39032278	Nonsense_Mutation	rs765057107	R375*	0.31
UCEC	chr22	39022970	Nonsense_Mutation	novel	R56*	0.13
UCEC	chr22	39025627	Silent	novel	D187D	0.31
UCEC	chr22	39032463	3'UTR	novel		0.29
UCEC	chr22	39029423	Missense_Mutation	novel	K222N	0.26
UCEC	chr22	39025173	Nonsense_Mutation	novel	S105*	0.05
UCEC	chr22	39032201	Missense_Mutation	NA	F349C	0.28
UCEC	chr22	39029504	Silent	rs776631266	G249G	0.28
UCEC	chr22	39032266	Nonsense_Mutation	novel	Q371*	0.45
UCEC	chr22	39025650	Missense_Mutation	rs375389371	R195H	0.28	APOBEC_N
UCEC	chr22	39031761	Missense_Mutation	NA	S277Y	0.11
UCEC	chr22	39022998	Missense_Mutation	rs759937585	S65L	0.33
UCEC	chr22	39025274	Missense_Mutation	rs61752258	R139W	0.4	APOBEC_N
UCEC	chr22	39025610	Missense_Mutation	novel	P182S	0.3	APOBEC_N

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
PCPG	DEL	0.3272	0.044123
THCA	DEL	0.1563	0.046486
THYM	DEL	0.0813	0.063154

Survival Analysis

Cancer	P-value	Q-value
KIRC	0.0001	Kaplan-Meier Survival Analysis
SARC	0.00053	Kaplan-Meier Survival Analysis
ACC	0.00026	Kaplan-Meier Survival Analysis
HNSC	0.048	Kaplan-Meier Survival Analysis
SKCM	0.00013	Kaplan-Meier Survival Analysis
BRCA	0.00011	Kaplan-Meier Survival Analysis
BLCA	0.00013	Kaplan-Meier Survival Analysis
CESC	0.00011	Kaplan-Meier Survival Analysis
UCEC	0.0057	Kaplan-Meier Survival Analysis
GBM	0.028	Kaplan-Meier Survival Analysis
THCA	0.042	Kaplan-Meier Survival Analysis
UVM	0.00014	Kaplan-Meier Survival Analysis