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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000248572 Accession number: AJ539163 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Xylosyltransferase 1.
 
 

Transcript original information
Accession number AJ539163.1
CAGE tag ID NA
EST ID NA
Clone Number NA
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (XYLT1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (XYLT1);
Sequence data provider NA
Annotation project NA
Length of cDNA 4207[bp] (No. of exon:12)[A:934 T:786 G:1213 C:1272]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type NA
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 4184(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGCAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0012845
Genomic location  G-integra Help Chromosome 16
Location 16p12.3
Position 17201341- 17564738
Strand -
Possible duplicated location(s) NA
Gene structure 12 exon(s)
Database links RefSeq NM_022166; 
Ensembl ENST00000261381; 
Entrez Gene Entrez Gene ID:64131; 
KEGG GENES KEGG GENES(64131); 
GeneCard GeneCardXYLT1;  *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 HIP000109786
Predicted CDS 86..2965;  959[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.824
Database links RefSeq NP_071449; 
UniProt Q86Y38; 
CCDS CCDS10569; 

Motif information
ORF

length(959),orf(86:2965) MVAAPCARRLARRSHSALLAALTVLLLQTLVVWNFSSLDSGAGERRGGAA VGGGEQPPPAPAPRRERRDLPAEPAAARGGGGGGGGGGGGRGPQARARGG GPGEPRGQQPASRGALPARALDPHPSPLITLETQDGYFSHRPKEKVRTDS NNENSVPKDFENVDNSNFAPRTQKQKHQPELAKKPPSRQKELLKRKLEQQ EKGKGHTFPGKGPGEVLPPGDRAAANSSHGKDVSRPPHARKTGGSSPETK YDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRF CPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIY HKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLST YLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKS HGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNR RFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNL RITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKF EAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLT LYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLI KHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDAKE RLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIE STAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPI KPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGT ALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELG AVKPDGRLR* 		a.a.
length		 InterPro Name
length(409), motif(322:730) 409 IPR003406 Glycosyl transferase, family 14 [Family]
length(253), motif(328:580) 253 IPR003406 Glycosyl transferase, family 14 [Family]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000248572
H-Inv cluster ID Locus viewHIX0012845
Accession number AJ539163.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript; 
Coding potential  Help Protein coding; 
Definition Xylosyltransferase 1.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_071449)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
Gene family/group Gene family H-Inv gene family/group ID HIF0002959
Gene family/group name Glycosyl transferase, family 14 (IPR003406).
Evidence motif (InterPro) ID IPR003406
Gene symbol/name HGNC symbol XYLT1
HGNC aliases NA
HGNC name xylosyltransferase I
DDBJ XYLT1
UniProt NA
EC number EC 2.4.2.26protein xylosyltransferase; 
GGDB
(GlycoGene Database)
 Gene symbol XYLT1
Familly Xylosyltransferases
Designation xylosyltransferase 1
Expression placenta
KEGG metabolic pathway 00532 :Chondroitin sulfate biosynthesis;  01030 :Glycan structures - biosynthesis 1; 
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000109786
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NM_022166; 
Ensembl ENST00000261381; 
Entrez Gene Entrez Gene ID:64131; 
KEGG GENES KEGG GENES(64131); 
GeneCard GeneCardXYLT1;  *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 Glycosyl transferase, family 14 (IPR003406). 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

Gene ontology information
Molecular function acetylglucosaminyltransferase activity (GO:0008375); 
Cellular component membrane (GO:0016020); 

Subcellular localization information  Last modified:20-Apr-2012
WoLF PSORT endoplasmic;  golgi apparatus;  extracellular;  Other; 
Target P signal peptide
SOSUI soluble protein
TMHMM membrane 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:20-Apr-2012
Start End PDB_ID E-value Identity Coverage SCOP_ID
403 479 2b5dX1 2e-06 21.6 74/114 a.8.3.3
528 602 1s66L 1e-04 21.2 66/119 d.110.3.2
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:20-Apr-2012
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator		 AceGene AGhsB230419; 
Affymetrix
GeneChip		 HG-Focus NA
HG-U133 232574_at;  236190_at; 
HG-U133A NA
HG-U133A_2 NA
HG-U133B 232574_at;  236190_at; 
HG-U133_Plus_2 232574_at;  236190_at; 
HG-U95 75706_at; 
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D 75706_at; 
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 3650407;  3650410;  3650465;  3682458;  3682459;  3682461;  3682463;  3682465;  3682466;  3682468;  3682473;  3682484;  3682485;  3682495;  3682496;  3682522;  3682554;  3682555;  3682556; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P349321; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P349321;  A_32_P91385; 
Related H-InvDB links H-ANGELH-ANGEL;  DNAProbeLocatorDNAProbeLocator; 

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:20-Apr-2012
Disease relation Disease name: {Pseudoxanthoma elasticum, modifier of severity of} (264800); 
Related information in OMIM OMIM ID:  608124;  Title: XYLOSYLTRANSFERASE 1
Co-localized orphan diseases OMIM ID:  156850;  605013;  605021;  606668;  607339;  608558;  608903;  610260; 
Disease related mutation MutationView:  608124; 
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(64131)
Disease Entrez Gene ID:(64131)
Substance Entrez Gene ID:(64131)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo Viewer;  LEGENDALEGENDA; 

Evolutionary information  Evola Help Last modified:20-Apr-2012
Relationship Species Accession number MGI Links
Orthology Rattus sp. (Rat) AJ295748 G-integraG-integra
Orthology Mus sp. (Mouse) AJ539164 MGI:2451073 G-integraG-integra
Orthology Canis sp. (Dog) AJ866719 G-integraG-integra
Orthology Oryzias sp. (Medaka) AM229407 G-integraG-integra
Orthology Gallus sp. (Chicken) AY619009 G-integraG-integra
Orthology Bos sp. (Cow) ENSBTAT00000007264 G-integraG-integra
Orthology Danio sp. (Zebrafish) ENSDART00000087131 G-integraG-integra
Orthology Equus sp. (Horse) ENSECAT00000006595 G-integraG-integra
Orthology Macaca sp. (Macaque) ENSMMUT00000024084 G-integraG-integra
Orthology Oryzias sp. (Medaka) ENSORLT00000016718 G-integraG-integra
Orthology Pongo sp. (Orangutan) ENSPPYT00000008404 G-integraG-integra
Orthology Pan sp. (Chimpanzee) ENSPTRT00000014408 G-integraG-integra
Orthology Tetraodon sp. (Tetraodon) GSTENT00021289001 G-integraG-integra
Orthology Tetraodon sp. (Tetraodon) GSTENT00022671001 G-integraG-integra
Orthology Takifugu sp. (Fugu) SINFRUT00000129411 G-integraG-integra
Orthology Takifugu sp. (Fugu) SINFRUT00000170555 G-integraG-integra
Orthology Monodelphis sp. (Opossum) XM_001365940 G-integraG-integra
Phylogenetic tree [View by ATV]
 Neighbor-joining (phb) 
Related H-InvDB links EvolaEvola;  dN/dS (under constraction); 

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
81 .. 81 C/G rs117041807 - 5'UTR
227 .. 227 G/A rs112153162 - CDS Nonsynonymous[Gly48Ser]
428 .. 428 G/T rs61758388 + CDS Nonsynonymous[Ala115Ser]
506 .. 506 C/T rs74993523 - CDS Nonsynonymous[Arg141Trp]
691 .. 691 A/G rs114030556 - CDS Synonymous[Lys202Lys]
753 .. 753 C/G rs113276942 - CDS Nonsynonymous[Ala223Gly]
1096 .. 1096 T/G rs76816613 - CDS Synonymous[Arg337Arg]
1162 .. 1162 C/T rs35488326 - CDS Synonymous[His359His]
1239 .. 1239 C/T rs36098987 - CDS Nonsynonymous[Pro385Leu]
1356 ^ 1357 -/T rs34709724 - CDS
1369 .. 1369 C/G rs28709752 - CDS Synonymous[Pro428Pro]
1538 .. 1538 G/C rs4782030 + CDS Nonsynonymous[Glu485Gln]
1828 .. 1828 G/A rs34653270 - CDS Synonymous[Pro581Pro]
1939 .. 1939 G/T rs77836443 - CDS Synonymous[Gly618Gly]
1960 .. 1960 G/A rs117591688 - CDS Synonymous[Pro625Pro]
2026 ^ 2027 -/T rs34685043 - CDS
2074 .. 2074 T/C rs12708815 - CDS Synonymous[Ala663Ala]
2079 .. 2079 C/T rs79030430 - CDS Nonsynonymous[Thr665Met]
2266 .. 2266 C/T rs112238716 - CDS Synonymous[Ile727Ile]
2381 .. 2381 C/G rs12325439 - CDS Nonsynonymous[Pro766Ala]
2416 .. 2416 T/C rs7201590 - CDS Synonymous[Asn777Asn]
2455 .. 2455 C/A rs74750647 - CDS Synonymous[Val790Val]
2461 .. 2461 A/G rs111893236 - CDS Synonymous[Ala792Ala]
2600 .. 2600 G/A rs7200466 - CDS Nonsynonymous[Val839Ile]
2655 .. 2655 A/G rs79977646 - CDS Nonsynonymous[Lys857Arg]
2716 .. 2716 C/T rs34511974 - CDS Synonymous[Pro877Pro]
2740 .. 2740 C/T rs924260 + CDS Synonymous[Pro885Pro]
2760 .. 2760 G/A rs35309694 - CDS Nonsynonymous[Arg892Gln]
2907 .. 2907 T/A rs74326444 - CDS Nonsynonymous[Phe941Tyr]
2976 .. 2976 G/A rs13331954 - 3'UTR
3270 .. 3270 C/T rs115646104 - 3'UTR
3294 .. 3294 C/T rs78572807 - 3'UTR
3295 .. 3295 G/T rs116076710 - 3'UTR
3296 .. 3296 A/T rs115541059 - 3'UTR
3316 .. 3316 G/A rs114672233 - 3'UTR
3354 .. 3354 A/T rs80296970 - 3'UTR
3392 .. 3392 T/C rs116934543 - 3'UTR
3419 .. 3419 C/T rs73526133 - 3'UTR
3531 .. 3531 T/C rs7194453 - 3'UTR
3555 .. 3555 T/C rs7194437 - 3'UTR
3568 .. 3568 G/A rs7193724 - 3'UTR
3620 .. 3620 G/A rs59519766 - 3'UTR
3674 .. 3674 A/G rs77933211 - 3'UTR
3728 .. 3728 G/C rs79229316 - 3'UTR
3854 .. 3854 G/A rs7193152 - 3'UTR
3885 .. 3885 G/A rs115325628 - 3'UTR
3921 ^ 3922 -/A rs72469343 - 3'UTR
3987 .. 3987 C/T rs74584130 - 3'UTR
4001 .. 4001 G/A rs3812960 - 3'UTR
4079 .. 4079 G/A rs7192758 - 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
Location Variation Strand
318..332 (gag)5 +
341..355 (gga)5 +
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
Type Start End Strand
Charlie15a 3273 3498 -
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD); 
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer;