H-InvDB_9.0 released on May 27, 2015. Search by Keyword H-Inv ID (HIT) H-Inv cluster ID (HIX) H-Inv protein ID (HIP) H-Inv gene family/group (HIF) Accession number Chromosome number Chromosome band Definition* Data source ID --- CCDS ID dbSNP ID (rs number) EC number Ensembl ID EntrezGene ID FR ID FR Accession number GO ID GO name* HGNC gene symbol HGNC gene name* InterPro ID InterPro name* OMIM ID OMIM title* Pathway ID Pathway name* RefSeq (gene) ID RefSeq (protein) ID SCOP ID UniProt for Advanced Search

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H-Invitational ID: HIT000033609 Accession number: BC008042 Created date: 26-Mar-2013 Last modified: 27-May-2015 Definition: Similar to Tumor necrosis factor ligand superfamily member 13 isoform gamma proprotein.

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Transcript original information Accession number BC008042.2 CAGE tag ID NA EST ID NA Clone Number MGC:15176 IMAGE:3837834 Experimental resources   NBRC ; HGPD ; Antibody (TNFSF13) ; Catalog (TNFSF13); Sequence data provider Provider:MGC/NCI;  Annotation project H-Invitational FLcDNA Length of cDNA 1465[bp] (No. of exon:7)[A:321 T:315 G:392 C:437] Devision HUM Molecular type mRNA Library origin Cell type NA Tissue type Ovary, adenocarcinoma Develpmental stage NA

Sequence quality information CDS feature Complete CDS Kozak sequence NA PolyA Site: 1443(+) Signal: 1423-1427(+) Vector/adapter sequence NA Frame shift NA Remaining intron NA Splice site acceptor (NAGNAG) GAGCAG;  Transcript quality feature NA Notes NA

CAACCTTCTTCCCTTCTGCACCACTGCCCGTACCCTTACCCGCCCCGCCA CCTCCTTGCTACCCCACTCTTGAAACCACAGCTGTTGGCAGGGTCCCCAG CTCATGCCAGCCTCATCTCCTTTCTTGCTAGCCCCCAAAGGGCCTCCAGG CAACATGGGGGGCCCAGTCAGAGAGCCGGCACTCTCAGTTGCCCTCTGGT TGAGTTGGGGGGCAGCTCTGGGGGCCGTGGCTTGTGCCATGGCTCTGCTG ACCCAACAAACAGAGCTGCAGAGCCTCAGGAGAGAGGTGAGCCGGCTGCA GGGGACAGGAGGCCCCTCCCAGAATGGGGAAGGGTATCCCTGGCAGAGTC TCCCGGAGCAGAGTTCCGATGCCCTGGAAGCCTGGGAGAGTGGGGAGAGA TCCCGGAAAAGGAGAGCAGTGCTCACCCAAAAACAGAAGAAGCAGCACTC TGTCCTGCACCTGGTTCCCATTAACGCCACCTCCAAGGATGACTCCGATG TGACAGAGGTGATGTGGCAACCAGCTCTTAGGCGTGGGAGAGGCCTACAG GCCCAAGGATATGGTGTCCGAATCCAGGATGCTGGAGTTTATCTGCTGTA TAGCCAGGTCCTGTTTCAAGACGTGACTTTCACCATGGGTCAGGTGGTGT CTCGAGAAGGCCAAGGAAGGCAGGAGACTCTATTCCGATGTATAAGAAGT ATGCCCTCCCACCCGGACCGGGCCTACAACAGCTGCTATAGCGCAGGTGT CTTCCATTTACACCAAGGGGATATTCTGAGTGTCATAATTCCCCGGGCAA GGGCGAAACTTAACCTCTCTCCACATGGAACCTTCCTGGGACTTTGATTT TACGGATATCTTGCTTCTGTTCCCCATGGAGCTCCGAATTCTTGCGTGTG TGTAGATGAGGGGCGGGGGACGGGCGCCAGGCATTGTCCAGACCTGGTCG GGGCCCACTGGAAGCATCCAGAACAGCACCACCATCTAGCGGCCGCTCGA GGGAAGCACCCGCCGGTTGGCCGAAGTCCACGAAGCCGCCCTCTGCTAGG GAAAACCCCTGGTTCTCCATGCCACACCTCTCTCCAGGTGCCCTCTGCCT CTTCACCCCACAAGAAGCCTTATCCTACGTCCTTCTCTCCATCTATCGGA CCCCAGTTTCCATCACTATCTCCAGAGATGTAGCTATTATGCGCCCGTCT ACAGGGGGTGCCCGACGATGACGGTGCCTTCGCAGTCAAATTACTCTTCG GGTCCCAAGGTTTGGCTTTCACGCGCTCCATTGCCCCGGCGTGGCAGGCC ATTCCAAGCCCTTCCGGGCTGGAACTGGTGTCGGAGGAGCCTCGGGTGTA TCGTACGCCCTGGTGTTGGTGTTGCCTCACTCCTCTGAGCTCTTCTTTCT GATCAAGCCCTGCTTAAAGTTAAATAAAATAGAATGAATGATAAAAAAAA AAAAAAAAAAAAAAA

Gene structure information

H-Inv cluster ID		HIX0013500
Genomic location	Chromosome	17
	Location	17p13.1
	Position	7462254- 7464918
	Strand	+
Possible duplicated location(s)		NA
Gene structure		7 exon(s)
Database links	RefSeq	NA
	Ensembl	NA
	Entrez Gene	Entrez Gene ID:8741;
	KEGG GENES	KEGG GENES(8741);
	GeneCard	TNFSF13;  *GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links		H-DBAS;  G-integra;  cDNA-genome alignment;

Predicted CDS information HIP ID HIP000082797 Predicted CDS 104..847;  247[aa];  Orientation:+2;  Codon Adaptation Index (CAI). 0.757

MPASSPFLLAPKGPPGNMGGPVREPALSVALWLSWGAALGAVACAMALLT QQTELQSLRREVSRLQGTGGPSQNGEGYPWQSLPEQSSDALEAWESGERS RKRRAVLTQKQKKQHSVLHLVPINATSKDDSDVTEVMWQPALRRGRGLQA QGYGVRIQDAGVYLLYSQVLFQDVTFTMGQVVSREGQGRQETLFRCIRSM PSHPDRAYNSCYSAGVFHLHQGDILSVIIPRARAKLNLSPHGTFLGL*

Motif information

	a.a. length	InterPro	Name
	134	IPR008983	Tumour necrosis factor-like domain [Domain]
	133	IPR008983	Tumour necrosis factor-like domain [Domain]
	132	IPR006052	Tumour necrosis factor domain [Domain]
	131	IPR006052	Tumour necrosis factor domain [Domain]
	101	IPR006052	Tumour necrosis factor domain [Domain]
	17	IPR021184	Tumour necrosis factor, conserved site [Conserved_site]

Gene function information

H-Inv ID		HIT000033609
H-Inv cluster ID		HIX0013500
Accession number		BC008042.2
CAGE tag ID		NA
EST ID		NA
Transcript feature		NO;
Coding potential		Protein coding;
Definition		Similar to Tumor necrosis factor ligand superfamily member 13 isoform gamma proprotein.
Similarity category		Category: Similar to known protein(Category II).
		Similar to known protein (NP_742085)  [Identity/coverage = 99.595%/100.0%] to Homo sapiens protein.
Experimental evidence		Protein evidence
PubMed ID		NA
Gene family/group	H-Inv gene family/group ID	NA
	Gene family/group name	NA
	Evidence motif (InterPro) ID	NA
Gene symbol/name	HGNC symbol	TNFSF13
	HGNC aliases	NA
	HGNC name	tumor necrosis factor (ligand) superfamily, member 13
	DDBJ	TNFSF13
	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)	H-Inv protein ID	HIP000082797
	No. of interaction	14
	Interaction partner(s)	HIP000022035;  HIP000022049;  HIP000030471;  HIP000032450;  HIP000036913;  HIP000036913;  HIP000039653;  HIP000040680;  HIP000041686;  HIP000057536;  HIP000064456;  HIP000075877;  HIP000079240;  HIP000083074;
	BIND	NA
	DIP	11062E;  11067E;
	MINT	NA
	HPRD	04122;  05365;
	IntAct	NA
Database links	RefSeq	NA
	Ensembl	NA
	Entrez Gene	Entrez Gene ID:8741;
	KEGG GENES	KEGG GENES(8741);
	GeneCard	TNFSF13;  *GeneCards is provided free to academic non-profit institutions.
	etc	Human-Gene diversity Of Life-style related Diseases;
Curation status		Auto-annotated
Notes		NA
Related H-InvDB links		Gene family;  Similarity Search Tool;  TACT;

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	tumor necrosis factor receptor binding (GO:0005164);  protein binding (GO:0005515);
Biological process	immune response (GO:0006955);
Cellular component	membrane (GO:0016020);

Subcellular localization information

Last modified:27-May-2015

WoLF PSORT	peroxisome;  cytosol;  mitochondria;  Other;
Target P	signal peptide
SOSUI	soluble protein
TMHMM	membrane protein
PTS1	Not targeted
Related H-InvDB links	LIFEdb;  JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP)

Last modified:27-May-2015

Start End PDB_ID E-value Identity Coverage SCOP_ID 116 247 1jh5A 4e-25 35.4 130/144 b.22.1.1

Related H-InvDB links GTOP

Gene expression information

Last modified:27-May-2015

Tissue-specific expression			NA
Probe information	AceGene		AGhsB020918;  AGhsB230110;
	Affymetrix GeneChip	HG-Focus	209500_x_at;
		HG-U133	209499_x_at;  209500_x_at;  210314_x_at;  211495_x_at;  229326_at;
		HG-U133A	209499_x_at;  209500_x_at;  210314_x_at;  211495_x_at;
		HG-U133A_2	209499_x_at;  209500_x_at;  210314_x_at;  211495_x_at;
		HG-U133B	229326_at;
		HG-U133_Plus_2	209499_x_at;  209500_x_at;  210314_x_at;  211495_x_at;  229326_at;
		HG-U95	35287_at;  58644_at;
		HG-U95A	35287_at;
		HG-U95B	58644_at;
		HG-U95C	NA
		HG-U95D	NA
		HG-U95E	NA
		HG-U95Av2	NA
		HuEx-1_0	3708781;  3708782;  3708783;  3708785;  3708788;  3708789;  3708790;  3708791;  3708794;  3708795;  3708796;  3708797;  3743818;  3743820;
		HuGeneFL	NA
	Agilent	Human 1A Oligo Microarray:PGID215	A_23_P152620;
		Whole Human Genome Oligo Microarray:PGID247	A_23_P152620;
Related H-InvDB links			H-ANGEL;  DNAProbeLocator;

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information

Single Nucleotide Polymorphism (SNP) and indel  Location Variation dbSNP ID Strand CDS/UTR Translation 29 .. 29 C/T rs186358612 + 5'UTR 167 .. 167 G/C rs138476542 + CDS Nonsynonymous[Val22Leu] 215 .. 215 G/T rs201860460 + CDS Nonsynonymous[Ala38Ser] 216 .. 216 C/T rs142987696 + CDS Nonsynonymous[Ala38Val] 302 .. 302 G/A rs11552708 + CDS Nonsynonymous[Gly67Arg] 324 .. 324 A/G rs138823376 + CDS Nonsynonymous[Asn74Ser] 328 .. 328 G/C rs12942687 + CDS Synonymous[Gly75Gly] 390 .. 390 G/A rs3803800 + CDS Nonsynonymous[Ser96Asn] 475 .. 475 C/T rs138604224 + CDS Synonymous[Asn124Asn] 514 .. 514 G/A rs148497612 + CDS Nonsynonymous[Met137Ile] 531 .. 531 G/- rs34476700 + CDS 582 .. 582 C/T rs7503669 + CDS Nonsynonymous[Ala160Val] 683 .. 683 T/C rs145345809 + CDS Nonsynonymous[Phe194Leu] 692 .. 692 A/G rs147443869 + CDS Nonsynonymous[Ile197Val] 706 .. 706 C/T rs61760045 + CDS Synonymous[Pro201Pro] 714 .. 714 C/T rs139748549 + CDS Nonsynonymous[Pro204Leu] 717 .. 717 A/T rs141602266 + CDS Nonsynonymous[Asp205Val] 719 .. 719 C/T rs201011600 + CDS Nonsynonymous[Arg206Trp] 725 .. 725 T/G rs145250389 + CDS Nonsynonymous[Tyr208Asp] 791 ^ 792 -/C rs34362644 + CDS 805 .. 805 G/A rs150976338 + CDS Synonymous[Ala234Ala] 872 .. 872 C/T rs201836244 + 3'UTR 872 ^ 873 -/C rs35424738 + 3'UTR 938 .. 938 C/T rs6608 + 3'UTR 1099 .. 1099 C/T rs189608582 + 3'UTR 1143 .. 1143 C/T rs138292852 + 3'UTR 1281 .. 1281 T/C rs183950986 + 3'UTR 1296 ^ 1297 -/G rs149819305 + 3'UTR 1407 .. 1407 G/A rs149609747 + 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  No data available Database links Human-Gene diversity Of Life-style related Diseases(H-GOLD);  Related H-InvDB links VaryGene;  Repeat Mask Viewer;