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Protein

PDZ domain-containing protein 7

Gene

PDZD7

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

Functioni

GO - Biological processi

Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
PDZ domain-containing protein 7
Gene namesi
Name:PDZD7
Synonyms:PDZK7
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:26257. PDZD7.

Subcellular locationi

GO - Cellular componenti

  • cilium Source: UniProtKB
  • extracellular space Source: UniProtKB
  • nucleus Source: UniProtKB
  • stereocilia ankle link Source: Ensembl
  • USH2 complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cell projection, Cilium, Nucleus

Pathology & Biotechi

Involvement in diseasei

A chromosomal aberration disrupting PDZD7 has been found in patients with non-syndromic sensorineural deafness. Translocation t(10;11),t(10;11).

Usher syndrome 2C (USH2C)1 Publication
The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. PDZD7 mutations have been found in combination with mutations in USH2A and GPR98 in patients affected by Usher syndrome, suggesting a role as contributor to digenic Usher syndrome or a modifier of retinal disease expression.1 Publication
Disease descriptionUSH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses.
See also OMIM:605472

Keywords - Diseasei

Deafness, Retinitis pigmentosa, Usher syndrome

Organism-specific databases

MalaCardsiPDZD7.
MIMi605472. phenotype.
Orphaneti231178. Usher syndrome type 2.
PharmGKBiPA142671189.

Polymorphism and mutation databases

BioMutaiPDZD7.
DMDMi73621380.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 517517PDZ domain-containing protein 7PRO_0000058297Add
BLAST

Proteomic databases

PaxDbiQ9H5P4.
PeptideAtlasiQ9H5P4.
PRIDEiQ9H5P4.

PTM databases

iPTMnetiQ9H5P4.
PhosphoSiteiQ9H5P4.

Expressioni

Tissue specificityi

Weakly expressed in the inner ear. Expressed in the retinal pigment epithelium.2 Publications

Gene expression databases

BgeeiQ9H5P4.
CleanExiHS_PDZD7.
ExpressionAtlasiQ9H5P4. baseline and differential.
GenevisibleiQ9H5P4. HS.

Interactioni

Subunit structurei

Interacts with USH1G. Interacts with GPR98. Interacts with USH2A.2 Publications

Protein-protein interaction databases

STRINGi9606.ENSP00000359234.

Structurei

Secondary structure

1
517
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi87 – 893Combined sources
Beta strandi93 – 964Combined sources
Beta strandi98 – 1025Combined sources
Beta strandi105 – 1084Combined sources
Beta strandi111 – 1166Combined sources
Helixi121 – 1255Combined sources
Beta strandi132 – 1365Combined sources
Helixi146 – 1549Combined sources
Beta strandi157 – 1659Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EEHNMR-A81-167[»]
ProteinModelPortaliQ9H5P4.
SMRiQ9H5P4. Positions 82-170, 222-289.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H5P4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini86 – 16883PDZ 1PROSITE-ProRule annotationAdd
BLAST
Domaini210 – 29384PDZ 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi319 – 34426Ser-richAdd
BLAST

Sequence similaritiesi

Contains 2 PDZ (DHR) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410ITA9. Eukaryota.
ENOG411197M. LUCA.
GeneTreeiENSGT00530000063178.
HOGENOMiHOG000115487.
HOVERGENiHBG082117.
InParanoidiQ9H5P4.
OMAiANGRYHR.
PhylomeDBiQ9H5P4.
TreeFamiTF325033.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
InterProiIPR001478. PDZ.
[Graphical view]
PfamiPF00595. PDZ. 2 hits.
[Graphical view]
SMARTiSM00228. PDZ. 2 hits.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 2 hits.
PROSITEiPS50106. PDZ. 2 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9H5P4-1) [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
MAQGFAVGFD PLGLGDLSSG SLSSLSSRGH LGSDSGSTAT RYLLRKQQRL
60 70 80 90 100
LNGPPRGIRA SSPMGRVILI NSPIEANSDE SDIIHSVRVE KSPAGRLGFS
110 120 130 140 150
VRGGSEHGLG IFVSKVEEGS SAERAGLCVG DKITEVNGLS LESTTMGSAV
160 170 180 190 200
KVLTSSSRLH MMVRRMGRVP GIKFSKEKTT WVDVVNRRLV VEKCGSTPSD
210 220 230 240 250
TSSEDGVRRI VHLYTTSDDF CLGFNIRGGK EFGLGIYVSK VDHGGLAEEN
260 270 280 290 300
GIKVGDQVLA ANGVRFDDIS HSQAVEVLKG QTHIMLTIKE TGRYPAYKEM
310 320 330 340 350
VSEYCWLDRL SNGVLQQLSP ASESSSSVSS CASSAPYSSG SLPSDRMDIC
360 370 380 390 400
LGQEEPGSRG PGWGRADTAM QTEPDAGGRV ETWCSVRPTV ILRDTAIRSD
410 420 430 440 450
GPHPGRRLDS ALSESPKTAL LLALSRPRPP ITRSQSYLTL WEEKQQRKKE
460 470 480 490 500
KSGSPGEKGA LQRSKTLMNL FFKGGRQGRL ARDGRREAWT LDSGSLAKTY
510
PRLDIEKEMG VSPCCPG
Length:517
Mass (Da):55,677
Last modified:March 1, 2001 - v1
Checksum:i06C9C614283478F7
GO
Isoform 2 (identifier: Q9H5P4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     511-512: VS → AT
     513-517: Missing.

Note: No experimental confirmation available.
Show »
Length:512
Mass (Da):55,205
Checksum:i0077E7435F2A7C99
GO
Isoform 3 (identifier: Q9H5P4-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     508-509: EM → AG
     512-517: SPCCPG → GPVQKFVTWR...SKPAPSPRIP

Show »
Length:1,033
Mass (Da):111,752
Checksum:iF267D0911E73ECBC
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti449 – 4491Missing in AAH29054 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei508 – 5092EM → AG in isoform 3. 1 PublicationVSP_039972
Alternative sequencei511 – 5122VS → AT in isoform 2. 1 PublicationVSP_015075
Alternative sequencei512 – 5176SPCCPG → GPVQKFVTWRLRRDQERGRA LLSARSGSPSSQLPNVDEQV QAWESRRPLIQDLAQRLLTD DEVLAVTRHCSRYVHEGGIE DLVRPLLAILDRPEKLLLLQ DIRSVVAPTDLGRFDSMVML VELEAFEALKSRAVRPPALR PARQDTPPKRHLITPVPDSR GGFYLLPVNGFPEEEDNGEL RERLGALKVSPSASAPRHPH KGIPPLQDVPVDAFTPLRIA CTPPPQLPPVAPRPLRPNWL LTEPLSREHPPQSQIRGRAQ SRSRSRSRSRSRSSRGQGKS PGRRSPSPVPTPAPSMTNGR YHKPRKARPPLPRPLDGEAA KVGAKQGPSESGTEGTAKEA AMKNPSGELKTVTLSKMKQS LGISISGGIESKVQPMVKIE KIFPGGAAFLSGALQAGFEL VAVDGENLEQVTHQRAVDTI RRAYRNKAREPMELVVRVPG PSPRPSPSDSSALTDGGLPA DHLPAHQPLDAAPVPAHWLP EPPTNPQTPPTDARLLQPTP SPAPSPALQTPDSKPAPSPR IP in isoform 3. 1 PublicationVSP_039973
Alternative sequencei513 – 5175Missing in isoform 2. 1 PublicationVSP_015076

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FJ617449 mRNA. Translation: ACU45386.1.
AK026862 mRNA. Translation: BAB15577.1.
AL133215 Genomic DNA. Translation: CAI10934.1.
BC029054 mRNA. Translation: AAH29054.1.
CCDSiCCDS31269.1. [Q9H5P4-1]
CCDS73182.1. [Q9H5P4-3]
RefSeqiNP_001182192.1. NM_001195263.1. [Q9H5P4-3]
NP_079171.1. NM_024895.4. [Q9H5P4-1]
XP_011538479.1. XM_011540177.1. [Q9H5P4-3]
UniGeneiHs.438245.

Genome annotation databases

EnsembliENST00000370215; ENSP00000359234; ENSG00000186862. [Q9H5P4-1]
ENST00000619208; ENSP00000480489; ENSG00000186862. [Q9H5P4-3]
GeneIDi79955.
KEGGihsa:79955.
UCSCiuc001kso.3. human. [Q9H5P4-1]

Keywords - Coding sequence diversityi

Alternative splicing, Chromosomal rearrangement

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FJ617449 mRNA. Translation: ACU45386.1.
AK026862 mRNA. Translation: BAB15577.1.
AL133215 Genomic DNA. Translation: CAI10934.1.
BC029054 mRNA. Translation: AAH29054.1.
CCDSiCCDS31269.1. [Q9H5P4-1]
CCDS73182.1. [Q9H5P4-3]
RefSeqiNP_001182192.1. NM_001195263.1. [Q9H5P4-3]
NP_079171.1. NM_024895.4. [Q9H5P4-1]
XP_011538479.1. XM_011540177.1. [Q9H5P4-3]
UniGeneiHs.438245.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EEHNMR-A81-167[»]
ProteinModelPortaliQ9H5P4.
SMRiQ9H5P4. Positions 82-170, 222-289.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000359234.

PTM databases

iPTMnetiQ9H5P4.
PhosphoSiteiQ9H5P4.

Polymorphism and mutation databases

BioMutaiPDZD7.
DMDMi73621380.

Proteomic databases

PaxDbiQ9H5P4.
PeptideAtlasiQ9H5P4.
PRIDEiQ9H5P4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000370215; ENSP00000359234; ENSG00000186862. [Q9H5P4-1]
ENST00000619208; ENSP00000480489; ENSG00000186862. [Q9H5P4-3]
GeneIDi79955.
KEGGihsa:79955.
UCSCiuc001kso.3. human. [Q9H5P4-1]

Organism-specific databases

CTDi79955.
GeneCardsiPDZD7.
HGNCiHGNC:26257. PDZD7.
MalaCardsiPDZD7.
MIMi605472. phenotype.
612971. gene.
neXtProtiNX_Q9H5P4.
Orphaneti231178. Usher syndrome type 2.
PharmGKBiPA142671189.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410ITA9. Eukaryota.
ENOG411197M. LUCA.
GeneTreeiENSGT00530000063178.
HOGENOMiHOG000115487.
HOVERGENiHBG082117.
InParanoidiQ9H5P4.
OMAiANGRYHR.
PhylomeDBiQ9H5P4.
TreeFamiTF325033.

Miscellaneous databases

EvolutionaryTraceiQ9H5P4.
GenomeRNAii79955.
PROiQ9H5P4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9H5P4.
CleanExiHS_PDZD7.
ExpressionAtlasiQ9H5P4. baseline and differential.
GenevisibleiQ9H5P4. HS.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
InterProiIPR001478. PDZ.
[Graphical view]
PfamiPF00595. PDZ. 2 hits.
[Graphical view]
SMARTiSM00228. PDZ. 2 hits.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 2 hits.
PROSITEiPS50106. PDZ. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), TISSUE SPECIFICITY, SUBCELLULAR LOCATION, INTERACTION WITH GPR98 AND USH2A, INVOLVEMENT IN USH2C.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  3. "The DNA sequence and comparative analysis of human chromosome 10."
    Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J.
    , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
    Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Brain.
  5. "Homozygous disruption of PDZD7 by reciprocal translocation in a consanguineous family: a new member of the Usher syndrome protein interactome causing congenital hearing impairment."
    Schneider E., Marker T., Daser A., Frey-Mahn G., Beyer V., Farcas R., Schneider-Ratzke B., Kohlschmidt N., Grossmann B., Bauss K., Napiontek U., Keilmann A., Bartsch O., Zechner U., Wolfrum U., Haaf T.
    Hum. Mol. Genet. 18:655-666(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, INTERACTION WITH USH1G, INVOLVEMENT IN DEAFNESS, CHROMOSOMAL TRANSLOCATION.
  6. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  7. "Solution structure of first PDZ domain of PDZ domain containing protein 7."
    RIKEN structural genomics initiative (RSGI)
    Submitted (AUG-2007) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 76-170.

Entry informationi

Entry nameiPDZD7_HUMAN
AccessioniPrimary (citable) accession number: Q9H5P4
Secondary accession number(s): D5FJ77, Q8N321
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 16, 2005
Last sequence update: March 1, 2001
Last modified: July 6, 2016
This is version 118 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.