H-InvDB x AHG DB
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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000052664 Accession number: BC042154 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Similar to Selenoprotein N; SelN; Precursor;
 
 

Transcript original information
Accession number BC042154.2
CAGE tag ID NA
EST ID NA
Clone Number IMAGE:4551053
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (SEPN1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (SEPN1);
Sequence data provider Provider:MGC/NCI; 
Annotation project H-Invitational FLcDNA
Length of cDNA 3015[bp] (No. of exon:4)[A:608 T:683 G:758 C:966]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Lung, large cell carcinoma
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature N-truncated
Kozak sequence NA
PolyA Site: 2999(+) Signal: 2980-2984(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0000278
Genomic location  G-integra Help Chromosome 1
Location 1p36.11
Position 26139177- 26144711
Strand +
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NM_019557;  NM_020451;  NM_206926;  NM_001099625;  NM_001099626;  NM_001099627; 
Ensembl ENST00000354177;  ENST00000361547;  ENST00000374300;  ENST00000374301;  ENST00000374303;  ENST00000374307;  ENST00000374315;  ENST00000388882;  ENST00000424294;  ENST00000464008;  ENST00000466284;  ENST00000469815;  ENST00000472643;  ENST00000474295;  ENST00000478284;  ENST00000488327;  ENST00000494293;  ENST00000494537;  ENST00000497956;  ENST00000524618;  ENST00000525713;  ENST00000526158;  ENST00000526894;  ENST00000527604;  ENST00000528624;  ENST00000529116;  ENST00000530599;  ENST00000531361;  ENST00000533762; 
Entrez Gene Entrez Gene ID:57190; 
KEGG GENES KEGG GENES(57190); 
GeneCard GeneCardSEPN1;  *GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS;  G-integraG-integra;  cDNA-genome alignmentcDNA-genome alignment; 

Predicted CDS information
HIP ID HIP000012927
Predicted CDS 107..493;  128[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.845

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000052664
H-Inv cluster ID Locus viewHIX0000278
Accession number BC042154.2
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Similar to Selenoprotein N; SelN; Precursor;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (Q9NZV5)  [Identity/coverage = 98.773%/27.63%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 10608886;  11528383;  12192640;  12700173;  15122708;  15489334;  16710414;  19067361;  ALL; 
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol SEPN1
HGNC aliases "rigid spine muscular dystrophy 1"
HGNC name selenoprotein N, 1
DDBJ SEPN1
UniProt SEPN1
EC number NA
GGDB
(GlycoGene Database)
 Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000012927
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NM_019557;  NM_020451;  NM_206926;  NM_001099625;  NM_001099626;  NM_001099627; 
Ensembl ENST00000354177;  ENST00000361547;  ENST00000374300;  ENST00000374301;  ENST00000374303;  ENST00000374307;  ENST00000374315;  ENST00000388882;  ENST00000424294;  ENST00000464008;  ENST00000466284;  ENST00000469815;  ENST00000472643;  ENST00000474295;  ENST00000478284;  ENST00000488327;  ENST00000494293;  ENST00000494537;  ENST00000497956;  ENST00000524618;  ENST00000525713;  ENST00000526158;  ENST00000526894;  ENST00000527604;  ENST00000528624;  ENST00000529116;  ENST00000530599;  ENST00000531361;  ENST00000533762; 
Entrez Gene Entrez Gene ID:57190; 
KEGG GENES KEGG GENES(57190); 
GeneCard GeneCardSEPN1;  *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases; 
Curation status Auto-annotated
Notes NA
Related H-InvDB links Gene familyGene family;  Similarity Search ToolSimilarity Search Tool;  TACTTACT; 
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA


Subcellular localization information  Last modified:20-Apr-2012
WoLF PSORT extracellular;  nuclear;  cytosol;  Other; 
Target P Not predicted
SOSUI soluble protein
TMHMM soluble protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Gene expression information  H-ANGEL DNAProbeLocator Last modified:20-Apr-2012
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator		 AceGene AGhsB041316; 
Affymetrix
GeneChip		 HG-Focus NA
HG-U133 224659_at; 
HG-U133A NA
HG-U133A_2 NA
HG-U133B 224659_at; 
HG-U133_Plus_2 224659_at; 
HG-U95 57716_at;  65964_at; 
HG-U95A NA
HG-U95B 57716_at; 
HG-U95C 65964_at; 
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2326143;  2326146;  2326147;  2326148;  2326149;  2326150;  2326151;  2326152;  2326153;  2326154;  2326156;  2402396;  2402397;  2402398;  2402399; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P370625; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P370625;  A_24_P231250; 
Related H-InvDB links H-ANGELH-ANGEL;  DNAProbeLocatorDNAProbeLocator; 

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:20-Apr-2012
Disease relation Disease name:NA
Related information in OMIM OMIM ID:NA Title:NA
Co-localized orphan diseases OMIM ID:  115665;  116600;  155600;  600975;  605225;  605606;  606788;  606852;  606928;  607317;  607671;  608543;  608553;  608995;  610320;  612367;  612596; 
Disease related mutation NA
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(57190)
Disease Entrez Gene ID:(57190)
Substance Entrez Gene ID:(57190)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo Viewer;  LEGENDALEGENDA; 

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
49 .. 49 G/A rs12023720 + 5'UTR
78 .. 78 G/C rs121908186 + 5'UTR
104 .. 104 T/G rs121908187 + 5'UTR
104 .. 106 TGA/- rs121908183 + 5'UTR
117 .. 117 G/A rs121908185 + CDS Nonsynonymous[Arg4Gln]
148 .. 148 G/A rs41284305 + CDS Synonymous[Ser14Ser]
226 .. 226 A/C rs2294228 - CDS Nonsynonymous[Lys40Asn]
257 .. 257 G/A rs61775004 + CDS Nonsynonymous[Gly51Ser]
465 .. 465 G/A rs74060854 + CDS Nonsynonymous[Arg120Gln]
537 .. 537 G/T rs116931343 + 3'UTR
637 .. 637 C/G rs58895091 + 3'UTR
721 .. 721 C/T rs115473437 + 3'UTR
760 .. 760 C/G rs77920263 + 3'UTR
994 .. 994 G/A rs112884056 + 3'UTR
1096 .. 1096 A/T rs1062256 + 3'UTR
1139 .. 1139 A/G rs12072426 + 3'UTR
1264 .. 1264 G/A rs80311079 + 3'UTR
1273 .. 1273 C/T rs11556312 + 3'UTR
1431 .. 1431 C/T rs116835124 + 3'UTR
1537 ^ 1538 -/TT rs71977125 + 3'UTR
1669 .. 1669 T/C rs75721508 + 3'UTR
1724 .. 1724 A/G rs113222117 + 3'UTR
1799 .. 1799 G/A rs117198314 + 3'UTR
1994 ^ 1995 -/TTTTG rs71810660 + 3'UTR
1998 .. 1998 G/A rs116792929 + 3'UTR
2003 ^ 2004 -/GTTTT rs72119467 + 3'UTR
2004 ^ 2005 -/TTTTG rs71761312 + 3'UTR
2008 .. 2008 G/T rs1062263 + 3'UTR
2013 ^ 2014 -/TTTTG rs56135183 + 3'UTR
2014 ^ 2015 -/TTTTG rs72428845 + 3'UTR
2110 .. 2110 C/T rs3203750 + 3'UTR
2220 .. 2220 C/T rs4659383 + 3'UTR
2261 .. 2261 C/G rs12404814 + 3'UTR
2280 .. 2280 C/G rs111634484 + 3'UTR
2541 .. 2541 G/T rs74060855 + 3'UTR
2628 .. 2628 C/T rs79324169 + 3'UTR
2713 .. 2714 CT/- rs71730380 + 3'UTR
2732 .. 2732 C/- rs75801637 + 3'UTR
2733 .. 2733 C/- rs11319301 + 3'UTR
2733 .. 2733 C/A rs78714889 + 3'UTR
2755 .. 2755 G/A rs6681307 + 3'UTR
2809 .. 2809 T/C rs58878991 + 3'UTR
2833 .. 2833 A/T rs1044183 + 3'UTR
2962 .. 2962 G/A rs6872 + 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
Location Variation Strand
1989..2013 (ttttg)5 +
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
Type Start End Strand
AluSx 1989 2294 -
MIRb 2332 2490 -
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD); 
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer;