Rbm39 MGI Mouse Gene Detail - MGI:2157953 - RNA binding motif protein 39

Rbm39 Gene Detail

Symbol

Rbm39
Name

RNA binding motif protein 39
Synonyms

1500012C14Rik, 2310040E03Rik, B330012G18Rik, caper, Caper alpha, Rnpc2

Feature Type

protein coding gene
IDs

MGI:2157953
NCBI Gene: 170791
Gene Overview

MyGene.info: RBM39

Sequence Map

Chr2:156147239-156180238 bp, - strand
From VEGA annotation of GRCm38

Mouse Genome Browser
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Sequence

33000 bp ± kb flank
Genome Browsers

VEGA | Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 77.36 cM
Mapping Data

3 experiments

Human Ortholog

RBM39, RNA binding motif protein 39

Vertebrate Orthologs

6

Human Ortholog

RBM39, RNA binding motif protein 39
Orthology source: HomoloGene, HGNC
Synonyms

CAPER, CAPERalpha, FSAP59, HCC1, RNPC2
Links

HGNC:15923

NCBI Gene ID: 9584

neXtProt AC: NX_Q14498
Chr Location

20q11.22; chr20:35703609-35742336 (-) GRCh38.p2

HomoloGene

Vertebrate Homology Class 136465
1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog
HCOP

human homology predictions: RBM39
Gene Tree

Rbm39

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Phenotype Summary

1 phenotype from 1 allele in 1 genetic background
7 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

162
Gene trapped

162
Incidental Mutations

Mutagenetix , APF , CvDC

Homozygous disruption of this locus results in embryonic lethality.

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All GO Annotations

16
GO References

4

External Resources

FuncBase

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	receptor	receptor binding	RNA binding	transcription	transferase	transporter

Biological Process

nucleic acid-templated transcription	carbohydrate derivative metabolism	cell death	cell differentiation	cell proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

73
Tissues

66
cDNA Data

26
Literature Summary

9

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO
Other Vertebrate Links

Xenbase rbm39

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Rbm39 interacts with 351 markers (Mir1a-1, Mir1a-2, Mir1b, ...) View All

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All Sequences

188
RefSeq

52
UniProt

15
CCDS

CCDS16964.1, CCDS71168.1

			Length	Strain/Species	Flank
genomic	OTTMUSG00000016122	VEGA Gene Model \| MGI Sequence Detail	33000	C57BL/6J	± kb
transcript	OTTMUST00000038535	VEGA \| MGI Sequence Detail	2810	Not Applicable
polypeptide	OTTMUSP00000017253	VEGA \| MGI Sequence Detail	530	Not Applicable

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SNPs within 2kb

173 from dbSNP Build 142

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UniProt

15 Sequences
Protein Ontology

PR:000013797 RNA-binding protein 39
PDB

2LQ5, 3S6E, 4J5O, 4RU2, 5CXT
InterPro Domains

IPR012677 Nucleotide-binding alpha-beta plait domain

IPR000504 RNA recognition motif domain

IPR003954 RNA recognition motif domain, eukaryote

IPR006509 Splicing factor, RBM39-like

IPR029123 Splicing factor RBM39, linker

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All nucleic 33

cDNA 32

Primer pair 1

Microarray probesets 12

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MGI:1914382, MGI:1923702, MGI:2139486, MGI:2139542, MGI:2443989

Summaries

All 41

Developmental Gene Expression 9

Gene Ontology 4

Phenotypes 7
Earliest

J:60984 Ko MS, et al., Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development. 2000 Apr;127(8):1737-49
Latest

J:213268 Kumar P P, et al., Coordinated control of senescence by lncRNA and a novel T-box3 co-repressor complex. Elife. 2014 May 29;:e02805

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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