H-InvDB_8.3 released on March 26, 2013. 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: HIT000330374 Accession number: AK222594 Created date: 26-Mar-2013 Last modified: 20-Apr-2012 Definition: Ribosomal protein S4, Y-linked 1 Y isoform variant; Fragment;

		Select format Flat file XML file Nucleotide sequence fasta Protein sequence fasta

Transcript original information Accession number AK222594.1 CAGE tag ID NA EST ID NA Clone Number CAS09424 Experimental resources   NBRC ; HGPD ; Antibody (RPS4Y1) ; Catalog (RPS4Y1); Sequence data provider NA Annotation project NA Length of cDNA 967[bp] (No. of exon:7)[A:326 T:226 G:227 C:188] Devision HUM Molecular type mRNA Library origin Cell type primary smooth muscle cells of human coronary artery Tissue type coronary artery Develpmental stage NA

Sequence quality information CDS feature Complete CDS Kozak sequence NA PolyA Site: 873(+) Signal: 852-856(+) Vector/adapter sequence NA Frame shift NA Remaining intron NA Splice site acceptor (NAGNAG) NA Transcript quality feature NA Notes NA

TCTCTTCCGTCGCAGAGTTTCGCCATGGCCCGGGGCCCCAAGAAGCACTT AAAGCGTGTTGCAGCGCCGAAGCATTGGATGCTTGACAAACTAACGGGTG TATTTGCACCTCGTCCATCGACAGGTCCCCACAAGCTGAGGGAATGTCTT CCTCTGATCGTCTTCCTCAGGAATAGACTCAAGTATGCGTTGACTGGAGA TGAGGTAAAGAAGATATGTATGCAACGTTTCATCAAAATTGATGGCAAGG TTCGAGTGGATGTCACATACCCTGCTGGATTCATGGATGTCATCAGCATC GAGAAGACAGGTGAACATTTCCGCCTGGTCTATGACACCAAGGGCCGTTT TGCTGTTCACCGCATCACAGTGGAAGAGGCAAAGTACAAGTTGTGCAAAG TGAGGAAGATTACTGTGGGAGTGAAGGGAATCCCTCACCTGGTGACTCAT GATGCTCGAACCATCCGCTACCCAGATCCTGTCATCAAGGTGAACGATAC TGTGCAGATTGATTTAGGGACTGGCAAGATAATCAACTTTATCAAATTTG ATACAGGCAATTTGTGTATGGTGATTGGTGGAGCCAACCTCGGTCGTGTT GGTGTGATCACCAACAGGGAAAGACATCCTGGTTCTTTTGGTGTGGTGCA TGTGAAGGATGCCAATGGCAACAGCTTTGCCACGAGGCTTTCCAACATTT TTGTCATTGGCAATGGCAATAAACCTTGGATTTCCCTGCCCAGGGGAAAG GGCATTCGACTTACTGTTGCTGAAGAGAGAGATAAGAGGCTGGCCACCAA ACAGAGCAGTGGCTAAATTGCAGTAGCAGCATATCTTTTTTTCTTTGCAC AAATAAACAGTGAATTCTCGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAA

Gene structure information

H-Inv cluster ID		HIX0017179
Genomic location	Chromosome	Y
	Location	Yp11.31
	Position	2709642- 2734991
	Strand	+
Possible duplicated location(s)		NA
Gene structure		7 exon(s)
Database links	RefSeq	NM_001008;
	Ensembl	ENST00000250784;  ENST00000430575;  ENST00000477725;  ENST00000515575;
	Entrez Gene	Entrez Gene ID:6192;
	KEGG GENES	KEGG GENES(6192);
	GeneCard	RPS4Y1;  *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 HIP000145418 Predicted CDS 25..816;  263[aa];  Orientation:+1;  Codon Adaptation Index (CAI). 0.755 Database links RefSeq NA UniProt Q53HI6;  CCDS NA

MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRN RLKYALTGDEVKKICMQRFIKIDGKVRVDVTYPAGFMDVISIEKTGEHFR LVYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYP DPVIKVNDTVQIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRER HPGSFGVVHVKDANGNSFATRLSNIFVIGNGNKPWISLPRGKGIRLTVAE ERDKRLATKQSSG*

Motif information

	a.a. length	InterPro	Name
	241	IPR000876	Ribosomal protein S4e [Family]
	262	IPR000876	Ribosomal protein S4e [Family]
	38	IPR013843	Ribosomal protein S4e, N-terminal [Domain]
	15	IPR018199	Ribosomal protein S4e, N-terminal, conserved site [Conserved_site]
	63	IPR002942	RNA-binding S4 [Domain]
	65	IPR002942	RNA-binding S4 [Domain]
	48	IPR002942	RNA-binding S4 [Domain]
	95	IPR013845	Ribosomal protein S4e, central [Domain]
	77	IPR013845	Ribosomal protein S4e, central [Domain]
	34	IPR005824	KOW [Domain]

Gene function information

H-Inv ID		HIT000330374
H-Inv cluster ID		HIX0017179
Accession number		AK222594.1
CAGE tag ID		NA
EST ID		NA
Transcript feature		NO;
Coding potential		Protein coding;
Definition		Ribosomal protein S4, Y-linked 1 Y isoform variant; Fragment;
Similarity category		Category: Identical to known human protein(Category I).
		Identical to known human protein (Q53HI6)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence		Protein evidence
PubMed ID		8125298;  9373149;  ALL;
Gene family/group	H-Inv gene family/group ID	HIF0000406
	Gene family/group name	Ribosomal protein S4e (IPR000876).
	Evidence motif (InterPro) ID	IPR000876
Gene symbol/name	HGNC symbol	RPS4Y1
	HGNC aliases	"ribosomal protein S4, Y-linked"
	HGNC name	ribosomal protein S4, Y-linked 1
	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)	H-Inv protein ID	HIP000145418
	No. of interaction	5
	Interaction partner(s)	HIP000057276;  HIP000068244;  HIP000091191;  HIP000257150;  HIP000381737;
	BIND	177539;
	DIP	NA
	MINT	MINT-64176;
	HPRD	00129;  00559;
	IntAct	EBI-2826885;  EBI-735516;
Database links	RefSeq	NM_001008;
	Ensembl	ENST00000250784;  ENST00000430575;  ENST00000477725;  ENST00000515575;
	Entrez Gene	Entrez Gene ID:6192;
	KEGG GENES	KEGG GENES(6192);
	GeneCard	RPS4Y1;  *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		Ribosomal protein S4e (IPR000876). 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	RNA binding (GO:0003723);  structural constituent of ribosome (GO:0003735);
Biological process	translation (GO:0006412);
Cellular component	intracellular (GO:0005622);  ribosome (GO:0005840);

Subcellular localization information

Last modified:20-Apr-2012

WoLF PSORT	cytosol;  mitochondria;
Target P	Not predicted
SOSUI	soluble protein
TMHMM	soluble 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:20-Apr-2012

Start End PDB_ID E-value Identity Coverage SCOP_ID 44 102 1h3eA2 5e-07 13.8 58/100 d.66.1.4

Related H-InvDB links GTOP

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 225 .. 225 A/G rs11538309 + CDS Synonymous[Gln67Gln] 451 .. 451 G/C rs11538308 + CDS Nonsynonymous[Asp143His] 471 .. 471 C/T rs72625370 + CDS Synonymous[Tyr149Tyr] 663 .. 663 C/T rs11538311 - CDS Synonymous[Ala213Ala] 735 .. 735 C/T rs35284970 + CDS Synonymous[Ser237Ser]  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;