Sfta3-ps (surfactant associated 3, pseudogene) - Rat Genome Database

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Gene: Sfta3-ps (surfactant associated 3, pseudogene) Mus musculus
Analyze
Symbol: Sfta3-ps
Name: surfactant associated 3, pseudogene
RGD ID: 1618251
MGI Page MGI
Description: Acts upstream of or within lung saccule development. Is expressed in brain; gut; heart; liver; and lung.
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AI413669; E030019B13Rik; hypothetical protein LOC104798; N; Nanci; RIKEN cDNA E030019B13 gene
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391256,537,213 - 56,576,205 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1256,535,106 - 56,576,373 (-)EnsemblGRCm39 Ensembl
GRCm381256,490,428 - 56,529,420 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1256,488,321 - 56,529,427 (-)EnsemblGRCm38mm10GRCm38
MGSCv371257,591,415 - 57,630,407 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361257,408,483 - 57,409,428 (-)NCBIMGSCv36mm8
Celera1257,639,031 - 57,678,757 (-)NCBICelera
Cytogenetic Map12C1NCBI
cM Map1224.4NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

References
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:16141072   PMID:16141073   PMID:24939938   PMID:28546511   PMID:30352852  


Genomics

Variants

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Variants in Sfta3-ps
1660 total Variants

QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121759644780956883Mouse
12832727Ahrq1_mairway hyperresponsiveness QTL 1 (mouse)125469591082665939Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121534102679040364Mouse
1300636Gct2_mgranulosa cell tumorigenesis 2 (mouse)Not determined122916068563160884Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121166000197176774Mouse
4141843Moen3_mmodifier of engrailed QTL 3 (mouse)Not determined122980158463801733Mouse
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12541844077031203Mouse
14747008Mancz10_mmandible centroid size 10 (mouse)122986352263863522Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
10402492Dipa8_mdrug induced psychomotor activation 8 (mouse)Not determined123493387268934019Mouse
1357749Vtbt13_mvertebral trabecular bone trait 13 (mouse)Not determined125313200287132145Mouse
12904004Opfaq11_mopen field activity QTL 11 (mouse)125315562457276756Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12955000084146774Mouse
1301989Hdlq18_mHDL QTL 18 (mouse)Not determined122916068563160884Mouse
1300818Bbaa10_mB.burgdorferi-associated arthritis 10 (mouse)Not determined123509100465511019Mouse
1357479Splwt1_mspleen weight 1 (mouse)Not determined124169317590887526Mouse
1357757Lnopy2_mlens opacity 2 (mouse)Not determined125284662686846796Mouse
12903999Opfaq8_mopen field activity QTL 8 (mouse)125490765357870585Mouse

Markers in Region
AI413669  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381256,490,618 - 56,490,714UniSTSGRCm38
MGSCv371257,591,605 - 57,591,701UniSTSGRCm37
Celera1257,639,221 - 57,639,317UniSTS
Cytogenetic Map12C1UniSTS
Whitehead/MRC_RH12579.41UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000218376
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,213 - 56,576,368 (-)Ensembl
GRCm38.p6 Ensembl1256,490,428 - 56,529,260 (-)Ensembl
RefSeq Acc Id: ENSMUST00000218497
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,258 - 56,552,470 (-)Ensembl
GRCm38.p6 Ensembl1256,490,473 - 56,505,685 (-)Ensembl
RefSeq Acc Id: ENSMUST00000219423
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,552,949 - 56,558,829 (-)Ensembl
GRCm38.p6 Ensembl1256,506,164 - 56,512,044 (-)Ensembl
RefSeq Acc Id: ENSMUST00000219680
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,535,106 - 56,540,109 (-)Ensembl
GRCm38.p6 Ensembl1256,488,321 - 56,493,324 (-)Ensembl
RefSeq Acc Id: ENSMUST00000220379
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,349 - 56,576,212 (-)Ensembl
GRCm38.p6 Ensembl1256,490,564 - 56,529,427 (-)Ensembl
RefSeq Acc Id: ENSMUST00000240836
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,213 - 56,576,373 (-)Ensembl
RefSeq Acc Id: ENSMUST00000241144
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,278 - 56,576,326 (-)Ensembl
RefSeq Acc Id: ENSMUST00000241321
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,257 - 56,576,237 (-)Ensembl
RefSeq Acc Id: ENSMUST00000241392
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,343 - 56,576,219 (-)Ensembl
RefSeq Acc Id: ENSMUST00000241715
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,257 - 56,576,205 (-)Ensembl
RefSeq Acc Id: ENSMUST00000241947
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,254 - 56,576,207 (-)Ensembl
RefSeq Acc Id: ENSMUST00000242002
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,273 - 56,576,268 (-)Ensembl
RefSeq Acc Id: ENSMUST00000242171
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,347 - 56,576,207 (-)Ensembl
RefSeq Acc Id: ENSMUST00000242917
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,254 - 56,576,167 (-)Ensembl
RefSeq Acc Id: ENSMUST00000243869
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,278 - 56,576,213 (-)Ensembl
RefSeq Acc Id: ENSMUST00000244036
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,239 - 56,576,214 (-)Ensembl
RefSeq Acc Id: ENSMUST00000244340
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,257 - 56,576,320 (-)Ensembl
RefSeq Acc Id: ENSMUST00000244611
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,343 - 56,576,218 (-)Ensembl
RefSeq Acc Id: ENSMUST00000244671
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,273 - 56,576,234 (-)Ensembl
RefSeq Acc Id: ENSMUST00000244991
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,278 - 56,568,099 (-)Ensembl
RefSeq Acc Id: ENSMUST00000245135
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,254 - 56,576,192 (-)Ensembl
RefSeq Acc Id: ENSMUST00000245149
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,278 - 56,576,284 (-)Ensembl
RefSeq Acc Id: ENSMUST00000245335
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,347 - 56,576,189 (-)Ensembl
RefSeq Acc Id: ENSMUST00000247117
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,254 - 56,576,214 (-)Ensembl
RefSeq Acc Id: ENSMUST00000247172
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1256,537,278 - 56,576,131 (-)Ensembl
RefSeq Acc Id: NR_045082
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391256,537,213 - 56,576,205 (-)NCBI
GRCm381256,490,428 - 56,529,420 (-)ENTREZGENE
Celera1257,639,031 - 57,678,757 (-)ENTREZGENE
cM Map12 ENTREZGENE
Sequence:
Promoters
RGD ID:15094109
Promoter ID:EPDNEWNC_M2021
Type:multiple initiation site
Name:Sfta3-ps_1
Description:surfactant associated 3, pseudogene [Source:MGISymbol;Acc:MGI:2144804]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381256,529,420 - 56,529,480EPDNEWNC
RGD ID:6822861
Promoter ID:MM_KWN:11696
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lung
Transcripts:AK138262_E030019B13RIK
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361257,594,751 - 57,595,251 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSMUSG00000112343 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000218376 ENTREZGENE
MGD MGI:2144804 ENTREZGENE
NCBI Gene 104798 ENTREZGENE
PhenoGen Sfta3-ps PhenoGen
RNAcentral URS0000759F29 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-11 Sfta3-ps  surfactant associated 3, pseudogene  E030019B13Rik  RIKEN cDNA E030019B13 gene  Symbol and/or name change 5135510 APPROVED