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PTCD1 Gene

protein-coding GIFtS: 43

GC07M098852

pentatricopeptide repeat domain 1
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases
KIAA0632 ^¹, ², ³

Descriptions
pentatricopeptide repeat domain 1 ^²

External Ids
HGNC: 22198¹
Entrez Gene: 26024²
UniProtKB: O75127³
Ensembl: ENSG00000106246⁷

Search outside databases for aliases for PTCD1 gene

Previous GC identifers: GC07M098626 GC07M098659

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the PTCD1 gene

Entrez Gene cytogenetic band: 7q22.1 Ensembl cytogenetic band: 7q22.1 HGNC cytogenetic band: 7q22.1

PTCD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 7 GeneLoc Exon Structure

GeneLoc location for GC07M098852: (about GC identifiers)

Start:	98,854,681 bp from pter
End:	98,874,355 bp from pter
Size:	19,675 bases
Orientation:	minus strand

1 alternative location:

Chr7-,CRA_TCAG 98,376,519-98,396,193

RefSeq DNA sequence:

NC_000007.12 NT_007933.14 NT_079595.2

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: PTCD1_HUMAN, O75127 (See protein sequence)

Recommended Name: Pentatricopeptide repeat-containing protein 1

Size: 700 amino acids; 78856 Da

Secondary accessions: Q3ZB78 Q66K60 Q9UDV2

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_056360.2

ENSEMBL proteins:

ENSP00000292478

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
	Browse Purified and Recombinant Proteins at Millipore
	Browse Human Recombinant Proteins at Sigma-Aldrich
	Browse R&D Systems for human recombinant proteins
	Browse recombinant and purified proteins available from Enzo Life Sciences
	Browse Abcam for Recombinant Proteins
	Browse Abnova for Human Recombinant Proteins

OriGene Purified Recombinant Human Protein: PTCD1

Antibodies for PTCD1:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for PTCD1
	Browse R&D Systems for Antibodies
	Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
	Browse Abnova for Monoclonal and Polyclonal Antibodies
	Search Novus for antibodies for PTCD1

Assays for PTCD1:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Graphical View of Domain Structure for InterPro Entry O75127

ProtoNet protein and cluster: O75127

UniProtKB/Swiss-Prot: PTCD1_HUMAN, O75127

Similarity: Contains 9 PPR (pentatricopeptide) repeats

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (PTCD1)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015545

Applied Biosystems Silencer® siRNAs for PTCD1

Sigma-Aldrich siRNA for PTCD1

Sigma-Aldrich shRNA for PTCD1

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for PTCD1
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_015545
Myc/DDK tagged cDNA clone in CMV expression vector: NM_015545
untagged cDNA clone in CMV expression vector: NM_015545

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_015545

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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3 Interacting proteins for PTCD1 (ENSP00000292478³) via UniProtKB, MINT, and/or STRING

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
PTCD3	ENSP00000254630³	STRING (score=.712)
PTCD2	ENSP00000370013³	STRING (score=.706)
--	ENSP00000370025³	STRING (score=.706)

About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for PTCD1

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (PTCD1)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015545

Sigma-Aldrich siRNA for PTCD1

Sigma-Aldrich shRNA for PTCD1

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_015545

REFSEQ mRNAs for PTCD1 gene:

NM_015545.2

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_015545

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_015545
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_015545
                                 untagged cDNA clone in CMV expression vector: NM_015545

Additional cDNA sequence:

AB014532.1 AB073644.1 AK001615.1 AK291004.1 AK295912.1 AK307981.1 BC003688.1 BC024042.1

BC080580.1 BC103495.1 BC103502.1 BC103661.1 CR598273.1

14 DOTS entries:

DT.102837314 DT.119015 DT.100760958 DT.121072369 DT.91703358 DT.100808868 DT.100812325 DT.121072141

DT.102837312 DT.102837322 DT.121072328 DT.70100295 DT.92443205 DT.121072433

24/116 AceView cDNA sequences (see all 116 ):

BU623604 BM793830 BX953527 AB014532 BU855942 CK820007 BQ051534 BM760549

BQ188261 BU185585 CR598273 CB306863 BM783321 AW615427 BM761673 BM273091

BC024042 AA773750 NM_015545 AI434682 BU500188 BQ934198 BU729750 BC080580

highest scoring ESTs for PTCD1:

AB014532 AL556225 AU132481 BE396456 BE514332 BG717613 BM468614 BM754448 BM754680 BU845809

Unigene Cluster for PTCD1:

Pentatricopeptide repeat domain 1

Hs.632313 [show with all ESTs]

Unigene Representative Sequence: AB014532

GeneLoc Exon Structure

3 Alternative Splicing Database (ASD) splice patterns (SP) for PTCD1

ExUns:	1a	·	1b	^	2a	·	2b	^	3a	·	3b	·	3c	^	4	^	5	^	6	^	7	^	8	^	9
SP1:					-		-
SP2:							-
SP3:

About this scheme

ECgene alternative splicing isoforms for PTCD1

1 Ensembl transcript including schematic representation:

ENST00000292478

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

PTCD1 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for PTCD1

¹ / ² / ³

4 probe-sets matching PTCD1 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
222796_at²^{, 3}	U133-B	1	1.00	1.00	--	--	AB014532	0.80	1.00	0.91	1
218956_s_at²^{, 3}	U133-A	1	1.00	1.00	--	--	NM_015545	0.60	1.00	0.82	1
222796_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
218956_s_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

About this table

Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: AAGGTAGAAC

SOURCE GeneReport for Unigene cluster: Hs.632313

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for PTCD1 gene from 5/7 species (see all 7 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	PTCD1¹	--	pentatricopeptide repeat domain 1	81.42(n) 77.73(a)	489860 XM_546978.2 XP_546978.2
chimpanzee (Pan troglodytes)	PTCD1¹	--	pentatricopeptide repeat domain 1	99.29(n) 98.57(a)	463571 XM_519233.2 XP_519233.2
mouse (Mus musculus)	Ptcd1^{1, 5}	5⁵	pentatricopeptide repeat domain 1^{1, 5}	79.43(n)¹ 74.53(a)¹	71799¹ NM_133735.1¹ NP_598496.2¹ AK004421⁵ AK088764⁵ (see all 28)
chicken (Gallus gallus)	PTCD1¹	--	pentatricopeptide repeat domain 1	62.47(n) 59.24(a)	416493 XM_414799.2 XP_414799.2
zebrafish (Danio rerio)	ptcd1¹	--	pentatricopeptide repeat domain 1	56.48(n) 50.8(a)	570247 XM_693706.3 XP_698798.1

About this table Species with no ortholog for PTCD1

ENSEMBL Gene Tree for PTCD1

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/79 NCBI SNPs in PTCD1 are shown (see all 79 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 38)

AB	SNP ID	Valid	Chr 7 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs34714513^1,2	C,F	98861024(-)	`TCAGCC/TCCCAG`	1	P/L	mis¹		5		NA EU EA WA	444
	rs35633728^1,2	C,F	98859395(-)	`CCCGGT/GGAACG`	1	G/V	mis¹		5		NA EU EA WA	436
--	rs10258918^1,2	H	98868928(+)	`GCAATC/TGCTCC`	1	R/Q	mis¹ ese³		4		EU EA WA	406
	rs940336^1,2	C,F,H	98870394(+)	`CAGTAC/TGGGGT`	1	P/P	syn¹ ese³		11		MN EA EU WA NA	2488
	rs2240384^1,2	A,C,F,H	98864980(-)	`TGGAGA/GTTGTG`	1	--	int¹		9		EA EU WA	2326
--	rs7794705^1,2	A,C,F,H	98867320(+)	`gtaggA/Gaaaag`	1	--	int¹ trp³		4		EU EA WA	416
	rs917154^1,2	A,C,F,H	98858742(-)	`AGTGGT/CGTCAT`	1	--	int¹		4		EU EA WA	418
	rs917153^1,2	C,F,H	98858939(-)	`CTCCCC/GCTTCC`	1	--	int¹ trp³		6		MN EA EU WA	2102
	rs10271049^1,2	A,F,H	98864429(+)	`GGGCTA/GAGCCG`	1	--	int¹		4		EU EA WA	416
--	rs11972285^1,2	A,C	98863527(+)	`actgcA/Ggaagg`	1	--	int¹		0	--	--	--	--

About this table

HapMap Linkage Disequilibrium images for PTCD1 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

7 PubMed articles for PTCD1 gene:

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{3, 4} Gerhard D.S....Malek J. (2004)
Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9734811)^{3, 4} Ishikawa K....Ohara O. (1998)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)³ Ota T....Sugano S. (2004)
Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)³ Scherer S.W....Tsui L.C. (2003)
The DNA sequence of human chromosome 7. (PubMed id 12853948)³ Hillier L.W.... Wilson R.K. (2003)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)³ Strausberg R.L....Marra M.A. (2002)
Toward a complete human genome sequence. (PubMed id 9847074)³ (1998)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 26024	HGNC: 22198	AceView: PTCD1	Ensembl:ENSG00000106246	euGenes: HUgn26024
ECgene: PTCD1	H-InvDB: PTCD1

(According to HUGE)
About This Section

HUGE: KIAA0632

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Licensable Technologies for PTCD1
(Available from WIS Yeda, Salk, Tufts)

About This Section

(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
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Products for PTCD1:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for PTCD1-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for PTCD1		Antibodies for PTCD1
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for PTCD1		Browse small molecules at Sigma-Aldrich
	"Your Favorite Gene" Pathways		feedback

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	Recombinant & Natural Proteins

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	Purified proteins from HEK293T cells
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	shRNA in GFP-retroviral vector

Search Tocris compounds for PTCD1

Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies

Search Novus for antibodies for PTCD1

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PTCD1 Gene

protein-coding GIFtS: 43

Aliases &
Descriptions
for PTCD1

Summaries
for PTCD1

Genomic Location
for PTCD1

Proteins
for PTCD1

Protein Domains/
Families
for PTCD1

Gene Function
for PTCD1

Pathways & Interactions
for PTCD1

Drugs & Compounds
for PTCD1

Transcripts
for PTCD1

Expression
for PTCD1

Orthologs
for PTCD1

Paralogs
for PTCD1

SNPs/Variants
for PTCD1

Disorders & Mutations
for PTCD1

Medical News
for PTCD1

Publications
for PTCD1

Search for PTCD1

Genome Databases showing PTCD1

Other Databases showing PTCD1

Specialized Databases showing PTCD1

Licensable Technologies
for PTCD1

Services
for PTCD1

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

PTCD1 Gene

protein-coding GIFtS: 43

Aliases & Descriptionsfor PTCD1

Summariesfor PTCD1

Genomic Locationfor PTCD1

Proteinsfor PTCD1

Protein Domains/Familiesfor PTCD1

Gene Functionfor PTCD1

Pathways & Interactionsfor PTCD1

Drugs & Compoundsfor PTCD1

Transcriptsfor PTCD1

Expression for PTCD1

Orthologsfor PTCD1

Paralogsfor PTCD1

SNPs/Variantsfor PTCD1

Disorders & Mutationsfor PTCD1

Medical Newsfor PTCD1

Publicationsfor PTCD1

Search for PTCD1

Genome Databases showing PTCD1

Other Databases showing PTCD1

Specialized Databases showing PTCD1

Licensable Technologiesfor PTCD1

Servicesfor PTCD1

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for PTCD1

Summaries
for PTCD1

Genomic Location
for PTCD1

Proteins
for PTCD1

Protein Domains/
Families
for PTCD1

Gene Function
for PTCD1

Pathways & Interactions
for PTCD1

Drugs & Compounds
for PTCD1

Transcripts
for PTCD1

Expression
for PTCD1

Orthologs
for PTCD1

Paralogs
for PTCD1

SNPs/Variants
for PTCD1

Disorders & Mutations
for PTCD1

Medical News
for PTCD1

Publications
for PTCD1

Licensable Technologies
for PTCD1

Services
for PTCD1