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Set Analyses:

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RBMY1F Gene

protein-coding GIFtS: 43
GCID: GC0YM024314

RNA Binding Motif Protein, Y-Linked, Family 1, Member F

See related diseases
at

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
RNA Binding Motif Protein, Y-Linked, Family 1, Member F¹ ²
Y Chromosome RNA Recognition Motif 2² ³
YRRM2² ³
RNA-Binding Motif Protein, Y Chromosome, Family 1 Member F/J²

External Ids:	HGNC: 23974¹	Entrez Gene: 159163²	Ensembl: ENSG00000169800⁷	UniProtKB: Q15415³

Export aliases for RBMY1F gene to outside databases

Previous GC identifers: GC0YP022795 GC0YM022724

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RBMY1F Gene:

This gene encodes a protein containing an RNA-binding motif in the N-terminus and four SRGY (serine, arginine,

glycine, tyrosine) boxes in the C-terminus. Multiple copies of this gene are found in the AZFb azoospermia factor

region of chromosome Y and the encoded protein is thought to be involved in spermatogenesis. Most copies of this

locus are pseudogenes, although six highly similar copies have full-length ORFs and are considered functional.

Four functional copies of this gene are found within inverted repeat IR2; two functional copies of this gene are

found in palindrome P3, along with two copies of PTPN13-like, Y-linked. (provided by RefSeq, Jul 2008)

GeneCards Summary for RBMY1F Gene:

RBMY1F (RNA binding motif protein, Y-linked, family 1, member F) is a protein-coding gene. Diseases associated with RBMY1F include azoospermia, and gonadoblastoma. An important paralog of this gene is RBMY1J.

UniProtKB/Swiss-Prot: RBY1F_HUMAN, Q15415

Function: RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly

by participating in pre-mRNA splicing in the testis

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:

NC_000024.10 NT_011903.12

Regulatory elements:

Regulatory transcription factor binding sites in the RBMY1F gene promoter:
POU2F1 POU2F1a
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: RBMY1F promoter sequence

Search Chromatin IP Primers for RBMY1F

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RBMY1F

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Yq11.223 Ensembl cytogenetic band: Yq11.223 HGNC cytogenetic band: Yq11.223

RBMY1F Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBMY1F gene location

GeneLoc information about chromosome Y GeneLoc Exon Structure

GeneLoc location for GC0YM024314: view genomic region (about GC identifiers)

Start:	24,314,689 bp from pter	End:	24,329,129 bp from pter
Size:	14,441 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: RBY1F_HUMAN, Q15415 (See protein sequence)

Recommended Name: RNA-binding motif protein, Y chromosome, family 1 member F/J

Size: 496 amino acids; 55728 Da

Subunit: Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3

Developmental stage: Expressed in all of the transcriptionally active stages of germ cell development from

spermatogonia through spermatocytes to round spermatids

Miscellaneous: The RBMY1 proteins are encoded by repeated regions of the Y chromosome, mostly within the AZFb

region. The exact number of functional copies is unclear and may vary between individuals, and some of them may

represent pseudogenes. The proteins are very similar, which makes the characterization of each protein difficult.

Thus, most experiments do not discriminate between the different members. One can therefore suppose that reported

interactions with a RBMY1 protein involve all the proteins

Secondary accessions: B2R916

Alternative splicing: 2 isoforms: Q15415-1 Q15415-2

Explore the universe of human proteins at neXtProt for RBMY1F: NX_Q15415

Explore proteomics data for RBMY1F at MOPED

Post-translational modifications:

Modification sites at neXtProt

Modification sites at PhosphoSitePlus

See RBMY1F Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_689798.1

ENSEMBL proteins:

ENSP00000307155 ENSP00000406005

RBMY1F Human Recombinant Protein Products:

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:

RBM: RNA binding motif (RRM) containing

3 InterPro protein domains:

IPR012604 RBM1CTR

IPR012677 Nucleotide-bd_a/b_plait

IPR000504 RRM_dom

Graphical View of Domain Structure for InterPro Entry Q15415

ProtoNet protein and cluster: Q15415

2 Blocks protein domains:

IPB000504 RNA-binding region RNP-1 (RNA recognition motif)

IPB012604 RBM1CTR

UniProtKB/Swiss-Prot: RBY1F_HUMAN, Q15415

Similarity: Contains 1 RRM (RNA recognition motif) domain

RBMY1F for domains About GeneDecksing

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: RBY1F_HUMAN, Q15415

Function: RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly

by participating in pre-mRNA splicing in the testis

Gene Ontology (GO): 3 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000166	nucleotide binding	--	--
GO:0003676	nucleic acid binding	--	--
GO:0003723	RNA binding	--	--

RBMY1F for ontologies About GeneDecksing

Animal Models:

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

RBY1F_HUMAN, Q15415: Nucleus

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
nucleus	5
cytosol	2

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Gene Ontology (GO): 2 cellular component terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005575	cellular_component	--	--
GO:0005634	nucleus	--	--

RBMY1F for ontologies About GeneDecksing

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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Custom Pathway & Disease-focused RT² Profiler PCR Arrays for RBMY1F
Interactions:

Search GeneGlobe Interaction Network for RBMY1F

STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

Selected Interacting proteins for RBMY1F (Q15415³ ENSP00000307155⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 13)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
HNRNPK	P61978³	I2D: score=1
BUD31	ENSP00000222969⁴	STRING: ENSP00000222969
CRNKL1	ENSP00000366557⁴	STRING: ENSP00000366557
ISY1	ENSP00000376973⁴	STRING: ENSP00000376973
PLRG1	ENSP00000303191⁴	STRING: ENSP00000303191

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Gene Ontology (GO): 3 biological process terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006397	mRNA processing	--	--
GO:0007283	spermatogenesis	--	--
GO:0008380	RNA splicing	--	--

RBMY1F for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for RBMY1F (RBY1F)

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for RBMY1F gene:

NM_152585.1

Unigene Cluster for RBMY1F:

RNA binding motif protein, Y-linked, family 1, member F

Hs.567746 [show with all ESTs]

Unigene Representative Sequence: NM_152585

3 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000303766(uc010nxh.3 uc004fva.3 uc022coi.1) ENST00000481858

ENST00000454978(uc022coh.1)

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Additional mRNA sequence:

AK313597.1 BC030018.2 BC152392.1 X76060.1

5 DOTS entries:

DT.207550 DT.120651216 DT.120654377 DT.120654921 DT.97826649

2 AceView cDNA sequences:

BC026077 BG718416

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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RBMY1F expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

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RBMY1F Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

RBMY1F Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.567746

UniProtKB/Swiss-Prot: RBY1F_HUMAN, Q15415

Tissue specificity: Testis-specific

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In Situ
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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for RBMY1F gene from Selected species (see all 10) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	RBMX⁶	Gallus gallus RNA binding motif protein, X-linked ...	62(a)	1 → many	4(4390057-4400409)
lizard (Anolis carolinensis)	Reptilia	--	Uncharacterized protein	58(a)	1 → many	GL343562.1(327293-337930)
zebrafish (Danio rerio)	Actinopterygii	rbmx⁶	RNA binding motif protein, X-linked	51(a)	1 → many	14(32725471-32732600) ENSDARG00000014244
fruit fly (Drosophila melanogaster)	Insecta	tra2⁶	transformer 2	15(a)	1 → many	2R(10489509-10491857)
worm (Caenorhabditis elegans)	Secernentea	rsp-8⁶	Protein RSP-8, isoform a	19(a)	1 → many	III(11826215-11831475) WBGene00004705

Species with no ortholog for RBMY1F

ENSEMBL Gene Tree for RBMY1F (if available)
TreeFam Gene Tree for RBMY1F (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for RBMY1F gene

RBMY1J¹ ² RBMY1A1¹ ² RBMY1B¹ ² RBMY1D¹ ² RBMY1E¹ ² TRA2B² RBMXL2² RBMXL3²

RBMXL1² CIRBP² RBM3² RBMX² TRA2A²

13 SIMAP similar genes for RBMY1F using alignment to 1 protein entry: RBY1F_HUMAN:

RBMY1B RBMY1A1 RBMY1C RBM RBMY1D RBMY1E

RBMY1J RBMX CIRBP RBMXL2 RBM38 RBM3

RBMXL1

RBMY1F for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr Y pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs376131297^1,2	C	--	24326955(+)	`AAAAT-/ACACACA`	1	--	int¹		0	--	--	--	--
rs370822321^1,2	--	--	24328613(+)	`CGACAC/TGTGCT`	1	--	int¹		0	--	--	--	--
rs368726541^1,2	--	--	24328649(+)	`CAGTGG/TTTAAG`	1	--	int¹		0	--	--	--	--
rs374664415^1,2	--	--	24328622(+)	`CTAACC/TAAAAG`	1	--	int¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for RBMY1F (24314689 - 24329129 bp)

Structural Variations
Database of Genomic Variants (DGV) Selected variations for RBMY1F (see all 11): About this table

Variant ID	Type	Subtype	PubMed ID
nsv515226	CNV	Loss	21397061
nsv471612	CNV	Loss	15918152
nsv10029	CNV	Gain	18304495
nsv10030	CNV	Gain	18304495
nsv10031	CNV	Gain	18304495
essv11423	CNV	CNV	17122850
essv15983	CNV	CNV	17122850
nsv442821	CNV	CNV	18776908
nsv442822	CNV	CNV	18776908
nsv515227	CNV	Complex	21397061

Site Specific Mutation Identification with PCR Assays

Search QIAGEN SeqTarget long-range PCR primers for resequencing RBMY1F

DNA2.0 Custom Variant and Variant Library Synthesis for RBMY1F

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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3 diseases for RBMY1F: About MalaCards

azoospermia gonadoblastoma turner syndrome

2 diseases from the University of Copenhagen DISEASES database for RBMY1F:

Gonadoblastoma Turner syndrome

RBMY1F for disorders About GeneDecksing

Export disorders for RBMY1F gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for RBMY1F gene integrated from 10 sources:
(articles sorted by number of sources associating them with RBMY1F)

Utopia: connect your pdf to the dynamic
world of online information

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)^{1, 2, 3} Skaletsky H.... Page D.C. (Nature 2003)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S.... Malek J. (Genome Res. 2004)
A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis. (PubMed id 8269511)^{1, 2} Ma K.... Jobling M. (Cell 1993)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)² Ota T.... Sugano S. (Nat. Genet. 2004)
RBMY, a male germ cell-specific RNA-binding protein, activated in human liver cancers and transforms rodent fibroblasts. (PubMed id 15184870)¹ Tsuei D.J....Chang M.H. (Oncogene 2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
RBMY, a probable human spermatogenesis factor, and other hnRNP G proteins interact with Tra2beta and affect splicing. (PubMed id 10749975)¹ Venables J.P....Eperon E.C. (Hum. Mol. Genet. 2000)
Structure and organization of the RBMY genes on the human Y chromosome: transposition and amplification of an ancestral autosomal hnRNPG gene. (PubMed id 9598316)¹ Chai N.-N.... Yen P.H. (Genomics 1998)
Degeneracy in human multicopy RBM (YRRM), a candidate spermatogenesis gene. (PubMed id 8875892)¹ Prosser J.... Cooke H.J. (Mamm. Genome 1996)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 159163	HGNC: 23974	AceView: MGC33094	Ensembl:ENSG00000169800	euGenes: HUgn159163
ECgene: RBMY1F	H-InvDB: RBMY1F

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for RBMY1F	Pharmacogenomics, SNPs, Pathways

Intellectual Property for RBMY1F gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for RBMY1F gene:
Search GeneIP for patents involving RBMY1F

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RBMY1F Gene

RNA Binding Motif Protein, Y-Linked, Family 1, Member F

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RBMY1F Gene

RNA Binding Motif Protein, Y-Linked, Family 1, Member F

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