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SFTA1P Gene

pseudogene   GIFtS: 22
GCID: GC10M010828

Surfactant Associated 1, Pseudogene

(Previous name: surfactant associated protein F)
(Previous symbol: SFTPF)
  Search for SFTA1P
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Surfactant Associated 1, Pseudogene1 2
SFTPF1 2
Surfactant Associated Protein F1

External Ids:    HGNC: 183831   Entrez Gene: 2071072   Ensembl: ENSG000002253837   

Export aliases for SFTA1P gene to outside databases

Previous GC identifers: GC10U901088 GC10M010827 GC10M010745


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SFTA1P Gene:
SFTA1P (surfactant associated 1, pseudogene) is a pseudogene.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000010.11  NC_018921.2  NT_008705.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the SFTA1P gene promoter:
         AP-2rep   NF-1   Pbx1a   HNF-4alpha2   IRF-1   Cdc5   HNF-4alpha1   HEN1   Nkx6-1   HSF2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SFTA1P


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10p14   Ensembl cytogenetic band:  10p14   HGNC cytogenetic band: 10p14

SFTA1P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SFTA1P gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M010828:  view genomic region     (about GC identifiers)

Start:
10,826,400 bp from pter      End:
10,836,943 bp from pter
Size:
10,544 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SFTA1P

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SFTA1P
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SFTA1P
Interactions:

    Search GeneGlobe Interaction Network for SFTA1P

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for SFTA1P



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Unigene Cluster for SFTA1P:

Surfactant associated 1, pseudogene
Hs.31562  [show with all ESTs]
Unigene Representative Sequence: BU601128
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602763(lincRNA) ENST00000415590(lincRNA) ENST00000434919(lincRNA) ENST00000446372(lincRNA)(uc001ikf.1)

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Additional mRNA sequence: 

AY102069.1 NR_027082.1 

4 DOTS entries:

DT.100018720  DT.100748612  DT.121262964  DT.100018721 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SFTA1P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TGGTTGAGGA
SFTA1P Expression
About this image


SFTA1P expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 4) fully expand
 
 Umbilical Cord (Extraembryonic Tissues)    fully expand to see all 2 entries
         Umbilical cord-derived mesenchymal stem cells (family)
 
 Mesenchymal Stem Cells (Uncategorized)    fully expand to see all 2 entries
         Umbilical cord-derived mesenchymal stem cells (family)
 
 Lung (Respiratory System)
         Basal Cells Respiratory Bronchioles
 
 Blood (Hematopoietic System)
         Umbilical cord blood-derived mesenchymal stem cells
SFTA1P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.31562
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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  --

ENSEMBL Gene Tree for SFTA1P (if available)
TreeFam Gene Tree for SFTA1P (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SFTA1P (see all 267)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 10 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1504795191,2
--10825906(+) AGATCA/GTGCCA 1 -- ds50010--------
rs1929196231,2
--10825956(+) AAAAAA/TAAAAA 1 -- ds50010--------
rs1152374941,2
C,F--10825958(+) AAAAAA/TAAATA 1 -- ds50011Minor allele frequency- T:0.04WA 118
rs1383102511,2
--10826099(+) TCCCTG/TAACCC 1 -- ds50010--------
rs1496466971,2
C--10826260(+) GTGTCC/TATGAC 1 -- ds50010--------
rs97141,2
C,F--10826500(+) ttctcC/Tgcagt 1 -- nc-transcript-variant18Minor allele frequency- T:0.48MN EA NA WA CSA 958
rs788732241,2
C,F--10826525(+) GCTAAT/CCTCCT 1 -- nc-transcript-variant3Minor allele frequency- C:0.12WA CSA 122
rs1449396541,2
C--10826571(+) CAGTCA/TCTCCT 1 -- nc-transcript-variant0--------
rs782261361,2
F--10826634(+) CTCCCT/GGTGGA 1 -- spa11Minor allele frequency- G:0.02EA 120
rs1388184771,2
--10826722(+) AGGAAA/TACCTG 1 -- int10--------

HapMap Linkage Disequilibrium report for SFTA1P (10826400 - 10836943 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SFTA1P: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SFTA1P
DNA2.0 Custom Variant and Variant Library Synthesis for SFTA1P

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with SFTA1P           About GenesLikeMe

Genetic Association Database (GAD): SFTA1P

Export disorders for SFTA1P gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SFTA1P gene integrated from 10 sources:
(articles sorted by number of sources associating them with SFTA1P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. GWAS of dental caries patterns in the permanent dentition. (PubMed id 23064961)1 Shaffer J.R....Marazita M.L. (J. Dent. Res. 2013)
  2. Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE. (PubMed id 21379329)4 Wijsman E.M....Mayeux R. (PLoS Genet. 2011)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
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, Kegg, and/or H-InvDB)
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Entrez Gene: 207107 HGNC: 18383 Ensembl:ENSG00000225383 euGenes: HUgn207107 ECgene: SFTA1P
H-InvDB: SFTA1P

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SFTA1P Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SFTA1P gene:
Search GeneIP for patents involving SFTA1P

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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