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

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
Alliance

gene page
Transcription Start Sites

10 TSS

Sequence Map

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

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 77.36 cM
Mapping Data

3 experiments

SNPs within 2kb

173 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2157953	protein coding gene	Chr2:156147239-156180238 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0026760	protein coding gene	Chr2:161009312-161052801 (-)
A/J	MGP_AJ_G0026726	protein coding gene	Chr2:154622524-154657110 (-)
AKR/J	MGP_AKRJ_G0026697	protein coding gene	Chr2:159105112-159138745 (-)
BALB/cJ	MGP_BALBcJ_G0026735	protein coding gene	Chr2:154907691-154944229 (-)
C3H/HeJ	MGP_C3HHeJ_G0026478	protein coding gene	Chr2:159464571-159498735 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0027184	protein coding gene	Chr2:165739364-165777823 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024554	protein coding gene	Chr2:148107222-148138707 (-)
CAST/EiJ	MGP_CASTEiJ_G0025939	protein coding gene	Chr2:159792977-159829842 (-)
CBA/J	MGP_CBAJ_G0026455	protein coding gene	Chr2:171763890-171803807 (-)
DBA/2J	MGP_DBA2J_G0026592	protein coding gene	Chr2:153794089-153827387 (-)
FVB/NJ	MGP_FVBNJ_G0026559	protein coding gene	Chr2:152167493-152201025 (-)
LP/J	MGP_LPJ_G0026697	protein coding gene	Chr2:161143422-161178603 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026580	protein coding gene	Chr2:175711815-175745825 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027240	protein coding gene	Chr2:158979287-159014710 (-)
PWK/PhJ	MGP_PWKPhJ_G0025673	protein coding gene	Chr2:153294642-153329052 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0025476	protein coding gene	Chr2:157919255-157952297 (-)
WSB/EiJ	MGP_WSBEiJ_G0026009	protein coding gene	Chr2:159868394-159905638 (-)

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

UniProt: Q14498
Chr Location

20q11.22; chr20:35703609-35742336 (-) GRCh38.p7

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
8 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	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

163
Endonuclease-mediated

1
Gene trapped

162
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

36 strains or lines available

Homozygous disruption of this locus results in embryonic lethality.

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All GO Annotations

21
GO References

5

External Resources

FuncBase

Molecular Function

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

Biological Process

carbohydrate derivative metabolism	cell death	cell differentiation	cell population proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	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

704
Tissues

66
cDNA Data

26
Literature Summary

10

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
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

217
RefSeq

104
UniProt

15
CCDS

CCDS16964.1, CCDS71168.1

Ensembl

ENSMUSG00000027620 (Evidence)
NCBI Gene

170791

			Length	Strain/Species	Flank
genomic	170791	NCBI Gene Model \| MGI Sequence Detail	33000	C57BL/6J	± kb
transcript	NM_001362766	RefSeq \| MGI Sequence Detail	3010	C57BL/6
polypeptide	Q8VH51	UniProt \| EBI \| MGI Sequence Detail	530	Not Applicable

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UniProt

15 Sequences
Protein Ontology

PR:000013797 RNA-binding protein 39

(term hierarchy)
PDB

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

IPR012677 Nucleotide-binding alpha-beta plait domain superfamily

IPR035979 RNA-binding domain superfamily

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 34

Genomic 1

cDNA 32

Primer pair 1

Microarray probesets 12

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

Summaries

All 45

Developmental Gene Expression 10

Gene Ontology 5

Phenotypes 8
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:256883 Zhou J, et al., Conserved expression of ultra-conserved noncoding RNA in mammalian nervous system. Biochim Biophys Acta. 2017 Dec;1860(12):1159-1168

TSS for Rbm39:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr27044	Chr2:156180135-156180201 (-)	70 bp
Tssr27043	Chr2:156179972-156179983 (-)	260 bp
Tssr27042	Chr2:156177763-156177780 (-)	2,466 bp
Tssr27039	Chr2:156174523-156174536 (-)	5,708 bp
Tssr27038	Chr2:156173727-156173731 (-)	6,509 bp
Tssr27037	Chr2:156173176-156173190 (-)	7,055 bp
Tssr27036	Chr2:156172991-156173024 (-)	7,230 bp
Tssr27035	Chr2:156167708-156167754 (-)	12,507 bp
Tssr27034	Chr2:156154294-156154295 (-)	25,943 bp
Tssr27033	Chr2:156152806-156152811 (-)	27,429 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer & Copyright Notice Send questions and comments to User Support.	last database update 01/05/2021 MGI 6.16