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Protein

PDZ domain-containing RING finger protein 4

Gene

PDZRN4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri18 – 5639RING-type; degeneratePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PDZ domain-containing RING finger protein 4
Alternative name(s):
Ligand of Numb protein X 4
SEMACAP3-like protein
Gene namesi
Name:PDZRN4
Synonyms:LNX4, SEMCAP3L
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:30552. PDZRN4.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134974780.

Polymorphism and mutation databases

BioMutaiPDZRN4.
DMDMi116242741.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10361036PDZ domain-containing RING finger protein 4PRO_0000055920Add
BLAST

Proteomic databases

PaxDbiQ6ZMN7.
PeptideAtlasiQ6ZMN7.
PRIDEiQ6ZMN7.

PTM databases

iPTMnetiQ6ZMN7.
PhosphoSiteiQ6ZMN7.

Expressioni

Gene expression databases

BgeeiENSG00000165966.
CleanExiHS_PDZRN4.
GenevisibleiQ6ZMN7. HS.

Organism-specific databases

HPAiHPA039510.

Interactioni

Protein-protein interaction databases

BioGridi118988. 3 interactions.
IntActiQ6ZMN7. 1 interaction.
MINTiMINT-3036691.
STRINGi9606.ENSP00000384197.

Structurei

3D structure databases

ProteinModelPortaliQ6ZMN7.
SMRiQ6ZMN7. Positions 223-322, 403-498.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini224 – 31491PDZ 1PROSITE-ProRule annotationAdd
BLAST
Domaini402 – 48685PDZ 2PROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili655 – 68935Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi116 – 16146Gly-richAdd
BLAST
Compositional biasi533 – 5364Poly-Glu
Compositional biasi957 – 9604Poly-Arg

Sequence similaritiesi

Contains 2 PDZ (DHR) domains.PROSITE-ProRule annotation
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri18 – 5639RING-type; degeneratePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG0297. Eukaryota.
KOG0312. Eukaryota.
ENOG410YT6N. LUCA.
GeneTreeiENSGT00510000046421.
HOGENOMiHOG000231379.
HOVERGENiHBG053554.
InParanoidiQ6ZMN7.
KOiK15682.
OMAiYEVSQVN.
OrthoDBiEOG091G0GKE.
PhylomeDBiQ6ZMN7.
TreeFamiTF315909.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
3.30.40.10. 1 hit.
3.90.890.10. 1 hit.
InterProiIPR001478. PDZ.
IPR013323. SIAH-type.
IPR008974. TRAF-like.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamiPF00595. PDZ. 2 hits.
[Graphical view]
SMARTiSM00228. PDZ. 2 hits.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMiSSF49599. SSF49599. 1 hit.
SSF50156. SSF50156. 2 hits.
PROSITEiPS50106. PDZ. 2 hits.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q6ZMN7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGFALERFAE AVDPALECKL CGQVLEEPLC TPCGHVFCAS CLLPWAVRRR
60 70 80 90 100
RCPLQCQPLA PGELYRVLPL RSLIQKLRVQ CDYRARGCGH SVRLHELEAH
110 120 130 140 150
VEHCDFGPAR RLRSRGGCAS GLGGGEVPAR GGCGPTPRAG RGGGARGGPP
160 170 180 190 200
GGRWGRGRGP GPRVLAWRRR EKALLAQLWA LQGEVQLTAR RYQEKFTQYM
210 220 230 240 250
AHVRNFVGDL GGGHRRDGEH KPFTIVLERE NDTLGFNIIG GRPNQNNQEG
260 270 280 290 300
TSTEGIYVSK ILENGPADRA DGLEIHDKIM EVNGKDLSKA THEEAVEAFR
310 320 330 340 350
NAKEPIVVQV LRRTPLSRPA YGMASEVQLM NASTQTDITF EHIMALAKLR
360 370 380 390 400
PPTPPVPDIC PFLLSDSCHS LHPMEHEFYE DNEYISSLPA DADRTEDFEY
410 420 430 440 450
EEVELCRVSS QEKLGLTVCY RTDDEEDTGI YVSEVDPNSI AAKDGRIREG
460 470 480 490 500
DRILQINGED VQNREEAVAL LSNDECKRIV LLVARPEIQL DEGWLEDERN
510 520 530 540 550
EFLEELNLEM LEEEHNEAMQ PTANEVEQPK KQEEEEGTTD TATSSSNNHE
560 570 580 590 600
KDSGVGRTDE SLRNDESSEQ ENAAEDPNST SLKSKRDLGQ SQDTLGSVEL
610 620 630 640 650
QYNESLVSGE YIDSDCIGNP DEDCERFRQL LELKCKIRNH GEYDLYYSSS
660 670 680 690 700
TIECNQGEQE GVEHELQLLN EELRNIELEC QNIMQAHRLQ KVTDQYGDIW
710 720 730 740 750
TLHDGGFRNY NTSIDMQRGK LDDIMEHPEK SDKDSSSAYN TAESCRSTPL
760 770 780 790 800
TVDRSPDSSL PRVINLTNKK NLRSTMAATQ SSSGQSSKES TSTKAKTTEQ
810 820 830 840 850
GCSAESKEKV LEGSKLPDQE KAVSEHIPYL SPYHSSSYRY ANIPAHARHY
860 870 880 890 900
QSYMQLIQQK SAVEYAQSQL SLVSMCKESQ KCSEPKMEWK VKIRSDGTRY
910 920 930 940 950
ITKRPVRDRI LKERALKIKE ERSGMTTDDD TMSEMKMGRY WSKEERKQHL
960 970 980 990 1000
VRAKEQRRRR EFMMRSRLEC LKESPQSGSE GKKEINIIEL SHKKMMKKRN
1010 1020 1030
KKILDNWMTI QELMTHGAKS PDGTRVHNAF LSVTTV
Length:1,036
Mass (Da):117,103
Last modified:October 17, 2006 - v3
Checksum:i26A43A0789CEA6B2
GO
Isoform 2 (identifier: Q6ZMN7-2) [UniParc]FASTAAdd to basket
Also known as: PDZRN4S

The sequence of this isoform differs from the canonical sequence as follows:
     1-258: Missing.
     259-281: SKILENGPADRADGLEIHDKIME → MGCNLCTFQKREEHYKLLYEVSQ

Show »
Length:778
Mass (Da):89,067
Checksum:iD7EDD0E1CBE6ABF2
GO
Isoform 4 (identifier: Q6ZMN7-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-260: Missing.
     261-281: ILENGPADRADGLEIHDKIME → MSGKRQFFLKPLALLTCWPST

Note: No experimental confirmation available.
Show »
Length:776
Mass (Da):88,672
Checksum:i726F2C05EB8B6700
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti650 – 6501S → G (PubMed:16541075).Curated
Sequence conflicti650 – 6501S → G in BAD18688 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti429 – 4291G → S.
Corresponds to variant rs285584 [ dbSNP | Ensembl ].
VAR_020966
Natural varianti784 – 7841G → R in a colorectal cancer sample; somatic mutation. 1 Publication
VAR_035951

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 260260Missing in isoform 4. 1 PublicationVSP_012614Add
BLAST
Alternative sequencei1 – 258258Missing in isoform 2. 1 PublicationVSP_012611Add
BLAST
Alternative sequencei259 – 28123SKILE…DKIME → MGCNLCTFQKREEHYKLLYE VSQ in isoform 2. 1 PublicationVSP_012612Add
BLAST
Alternative sequencei261 – 28121ILENG…DKIME → MSGKRQFFLKPLALLTCWPS T in isoform 4. 1 PublicationVSP_012615Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC090531 Genomic DNA. No translation available.
AC021651 Genomic DNA. No translation available.
AK131554 mRNA. Translation: BAD18688.1.
BC040922 mRNA. Translation: AAH40922.1.
BC093744 mRNA. Translation: AAH93744.1.
BC093746 mRNA. Translation: AAH93746.2.
BX640695 mRNA. Translation: CAE45818.2.
AL133067 mRNA. Translation: CAB61390.3.
CCDSiCCDS53777.1. [Q6ZMN7-1]
CCDS8739.1. [Q6ZMN7-2]
PIRiT42667.
RefSeqiNP_001158067.1. NM_001164595.1. [Q6ZMN7-1]
NP_037509.3. NM_013377.3. [Q6ZMN7-2]
UniGeneiHs.380044.

Genome annotation databases

EnsembliENST00000298919; ENSP00000298919; ENSG00000165966. [Q6ZMN7-4]
ENST00000402685; ENSP00000384197; ENSG00000165966. [Q6ZMN7-1]
ENST00000539469; ENSP00000439990; ENSG00000165966. [Q6ZMN7-2]
GeneIDi29951.
KEGGihsa:29951.
UCSCiuc001rmq.5. human. [Q6ZMN7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC090531 Genomic DNA. No translation available.
AC021651 Genomic DNA. No translation available.
AK131554 mRNA. Translation: BAD18688.1.
BC040922 mRNA. Translation: AAH40922.1.
BC093744 mRNA. Translation: AAH93744.1.
BC093746 mRNA. Translation: AAH93746.2.
BX640695 mRNA. Translation: CAE45818.2.
AL133067 mRNA. Translation: CAB61390.3.
CCDSiCCDS53777.1. [Q6ZMN7-1]
CCDS8739.1. [Q6ZMN7-2]
PIRiT42667.
RefSeqiNP_001158067.1. NM_001164595.1. [Q6ZMN7-1]
NP_037509.3. NM_013377.3. [Q6ZMN7-2]
UniGeneiHs.380044.

3D structure databases

ProteinModelPortaliQ6ZMN7.
SMRiQ6ZMN7. Positions 223-322, 403-498.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118988. 3 interactions.
IntActiQ6ZMN7. 1 interaction.
MINTiMINT-3036691.
STRINGi9606.ENSP00000384197.

PTM databases

iPTMnetiQ6ZMN7.
PhosphoSiteiQ6ZMN7.

Polymorphism and mutation databases

BioMutaiPDZRN4.
DMDMi116242741.

Proteomic databases

PaxDbiQ6ZMN7.
PeptideAtlasiQ6ZMN7.
PRIDEiQ6ZMN7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000298919; ENSP00000298919; ENSG00000165966. [Q6ZMN7-4]
ENST00000402685; ENSP00000384197; ENSG00000165966. [Q6ZMN7-1]
ENST00000539469; ENSP00000439990; ENSG00000165966. [Q6ZMN7-2]
GeneIDi29951.
KEGGihsa:29951.
UCSCiuc001rmq.5. human. [Q6ZMN7-1]

Organism-specific databases

CTDi29951.
GeneCardsiPDZRN4.
HGNCiHGNC:30552. PDZRN4.
HPAiHPA039510.
MIMi609730. gene.
neXtProtiNX_Q6ZMN7.
PharmGKBiPA134974780.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0297. Eukaryota.
KOG0312. Eukaryota.
ENOG410YT6N. LUCA.
GeneTreeiENSGT00510000046421.
HOGENOMiHOG000231379.
HOVERGENiHBG053554.
InParanoidiQ6ZMN7.
KOiK15682.
OMAiYEVSQVN.
OrthoDBiEOG091G0GKE.
PhylomeDBiQ6ZMN7.
TreeFamiTF315909.

Miscellaneous databases

ChiTaRSiPDZRN4. human.
GenomeRNAii29951.
PROiQ6ZMN7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000165966.
CleanExiHS_PDZRN4.
GenevisibleiQ6ZMN7. HS.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
3.30.40.10. 1 hit.
3.90.890.10. 1 hit.
InterProiIPR001478. PDZ.
IPR013323. SIAH-type.
IPR008974. TRAF-like.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamiPF00595. PDZ. 2 hits.
[Graphical view]
SMARTiSM00228. PDZ. 2 hits.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMiSSF49599. SSF49599. 1 hit.
SSF50156. SSF50156. 2 hits.
PROSITEiPS50106. PDZ. 2 hits.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPZRN4_HUMAN
AccessioniPrimary (citable) accession number: Q6ZMN7
Secondary accession number(s): Q52LY3
, Q52LY4, Q6N052, Q8IUU1, Q9NTP7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2005
Last sequence update: October 17, 2006
Last modified: September 7, 2016
This is version 121 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.