H-InvDB x AHG DB
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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000097316 Accession number: BC042673 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Conserved hypothetical protein.
 
 

Transcript original information
Accession number BC042673.1
CAGE tag ID NA
EST ID NA
Clone Number IMAGE:4826430
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (LINC00550) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (LINC00550);
Sequence data provider NA
Annotation project NA
Length of cDNA 3446[bp] (No. of exon:3)[A:1464 T:784 G:592 C:606]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Testis
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 3432(+) Signal: 3423-3427(+)
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 HIX0037526
Genomic location  G-integra Help Chromosome 13
Location 13q21.33
Position 69435418- 69459457
Strand -
Possible duplicated location(s) NA
Gene structure 3 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:338862
KEGG GENES KEGG GENES(338862)
GeneCard GeneCardLINC00550*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 HIP000448234
Predicted CDS 2342..2548;  68[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.733

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000097316
H-Inv cluster ID Locus viewHIX0037526
Accession number BC042673.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript; 
Coding potential  Help Protein coding; 
Definition Conserved hypothetical protein.
Similarity category  Help Category: Conserved hypothetical protein(Category IV).
Conserved hypothetical protein.
Experimental evidence NA
PubMed ID NA
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 LINC00550
HGNC aliases NA
HGNC name long intergenic non-protein coding RNA 550
DDBJ NA
UniProt NA
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 HIP000448234
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:338862
KEGG GENES KEGG GENES(338862)
GeneCard GeneCardLINC00550*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Human curated
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:27-May-2015
WoLF PSORT mitochondria;  cytosol;  extracellular;  Other; 
Target P Other
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.

Protein structure information (GTOP) GTOP Last modified:27-May-2015
Start End PDB_ID E-value Identity Coverage SCOP_ID
1 102 1vybA 1e-06 51.0 102/236 d.151.1.1
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene NA
Affymetrix
GeneChip
HG-Focus NA
HG-U133 NA
HG-U133A NA
HG-U133A_2 NA
HG-U133B NA
HG-U133_Plus_2 1557717_at; 
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2390293;  3517004;  3517006;  3517011; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 NA
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

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
9 .. 9 T/C rs2438444 + 5'UTR
11 .. 11 C/A rs115474797 - 5'UTR
21 .. 21 G/C rs2438445 + 5'UTR
32 .. 32 G/A rs7982349 - 5'UTR
281 .. 281 T/C rs61736705 - 5'UTR
500 ^ 501 -/A rs35940614 - 5'UTR
562 .. 562 A/G rs142908736 - 5'UTR
606 .. 606 G/T rs201950160 + 5'UTR
660 .. 660 A/T rs190199113 - 5'UTR
740 .. 740 G/A rs140474047 - 5'UTR
883 .. 883 C/T rs147201958 - 5'UTR
1023 .. 1023 A/G rs185877218 - 5'UTR
1032 .. 1032 A/G rs76952134 - 5'UTR
1066 .. 1066 G/T rs57656744 - 5'UTR
1091 .. 1091 T/G rs61584421 - 5'UTR
1194 .. 1194 T/C rs111445736 - 5'UTR
1223 .. 1223 G/A rs78812256 - 5'UTR
1263 .. 1263 C/T rs79073891 - 5'UTR
1269 .. 1269 A/G rs181436473 - 5'UTR
1374 .. 1374 A/G rs77630595 - 5'UTR
1438 .. 1438 T/C rs1583677 + 5'UTR
1454 .. 1454 A/G rs189099619 - 5'UTR
1742 .. 1742 C/T rs116452650 - 5'UTR
1754 .. 1754 G/A rs185547739 - 5'UTR
1772 .. 1772 G/C rs149481731 - 5'UTR
1805 .. 1805 A/G rs78598938 - 5'UTR
1847 .. 1847 T/C rs138006579 - 5'UTR
1855 .. 1855 G/A rs182209089 - 5'UTR
1866 ^ 1867 -/A rs151072768 - 5'UTR
1902 .. 1902 C/A rs113372999 - 5'UTR
2223 .. 2223 T/C rs190742415 - 5'UTR
2236 .. 2236 G/A rs184256094 - 5'UTR
2243 .. 2243 G/A rs138535811 - 5'UTR
2287 .. 2287 C/T rs145148663 - 5'UTR
2375 .. 2375 A/G rs111246565 - CDS Nonsynonymous[Ile12Val]
2558 .. 2558 A/G rs146602306 - 3'UTR
2686 .. 2686 T/C rs79806215 - 3'UTR
2757 .. 2757 C/T rs191446170 - 3'UTR
2781 .. 2781 A/G rs188539209 - 3'UTR
2800 .. 2800 G/T rs183996090 - 3'UTR
2809 .. 2809 A/G rs76356814 - 3'UTR
2892 .. 2892 T/A rs12017867 - 3'UTR
2923 .. 2923 A/C rs112615641 - 3'UTR
2944 .. 2944 G/A rs630878 + 3'UTR
2947 .. 2947 A/G rs148953609 - 3'UTR
2973 .. 2973 T/C rs191920097 - 3'UTR
3084 .. 3084 G/A rs188446963 - 3'UTR
3121 .. 3121 C/T rs183952119 - 3'UTR
3143 .. 3143 A/G rs111757647 - 3'UTR
3155 .. 3155 A/C rs632041 + 3'UTR
3202 .. 3202 C/A rs149800793 - 3'UTR
3203 .. 3203 C/T rs193061834 - 3'UTR
3260 .. 3260 T/C rs140677165 - 3'UTR
3286 .. 3286 G/T rs75252052 - 3'UTR
3315 .. 3315 A/G rs111956350 - 3'UTR
3361 .. 3361 A/C rs144492231 - 3'UTR
3371 .. 3371 G/A rs78988720 - 3'UTR
3379 .. 3379 T/C rs189202915 - 3'UTR
3381 .. 3381 G/A rs7491646 - 3'UTR
3388 .. 3388 A/G rs147192229 - 3'UTR
3397 .. 3397 C/A rs111772934 - 3'UTR
3415 .. 3415 C/A rs182553294 - 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
Type Start End Strand
MER54A 13 147 -
L1M2 300 776 +
L1M2 892 3432 +
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD)
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer