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
Alliance

genome feature page
Transcription Start Sites

12 TSS

Sequence Map

Chr2:155989159-156022158 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 77.36 cM
Mapping Data

3 experiments

SNPs within 2kb

716 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2157953	protein coding gene	Chr2:155989159-156022649 (-)
129S1/SvImJ	ENSMUSG00200016136	protein coding gene	Chr2:152855565-152887760 (-)
A/J	ENSMUSG00195018839	protein coding gene	Chr2:153217676-153249693 (-)
AKR/J	ENSMUSG00220012204	protein coding gene	Chr2:152507146-152539162 (-)
BALB/cJ	ENSMUSG00180045939	protein coding gene	Chr2:152685678-152717586 (-)
C3H/HeJ	ENSMUSG00175044314	protein coding gene	Chr2:153436077-153467977 (-)
C57BL/6NJ	ENSMUSG00215020577	protein coding gene	Chr2:152837391-152869394 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024554	protein coding gene	Chr2:148107222-148138707 (-)
CAST/EiJ	ENSTCUG00005043055	protein coding gene	Chr2:151822344-151854200 (-)
CBA/J	ENSMUSG00210016821	protein coding gene	Chr2:153367195-153399097 (-)
DBA/2J	ENSMUSG00185047165	protein coding gene	Chr2:153050499-153082506 (-)
FVB/NJ	ENSMUSG00205040924	protein coding gene	Chr2:152128759-152160656 (-)
JF1/MsJ	ENSUMUG00000023979	protein coding gene	Chr2:152706804-152738811 (-)
LP/J	ENSMUSG00230041110	protein coding gene	Chr2:154653424-154685618 (-)
NOD/ShiLtJ	ENSMUSG00190045354	protein coding gene	Chr2:152755674-152787578 (-)
NZO/HlLtJ	ENSMUSG00225004910	protein coding gene	Chr2:162682585-162714015 (-)
PWK/PhJ	ENSLUMG00010044472	protein coding gene	Chr2:152650531-152682486 (-)
SPRET/EiJ	ENSMSPG00010034012	protein coding gene	Chr2:155442878-155475171 (-)
WSB/EiJ	ENSIUOG00005041750	protein coding gene	Chr2:152441199-152473026 (-)

Human Ortholog

RBM39, RNA binding motif protein 39

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

RBM39, RNA binding motif protein 39
Synonyms

CAPER, CAPERalpha, FSAP59, HCC1, RNPC2
Links

HGNC:15923

NCBI Gene ID: 9584

UniProt: Q14498
Chr Location

20q11.22; chr20:35701347-35742312 (-) GRCh38

MGI Vertebrate Homology

Rbm39 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: RBM39
Gene Tree

Rbm39

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Phenotype Summary

8 phenotypes from 2 alleles in 2 genetic backgrounds
13 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

155
Endonuclease-mediated

6
Gene trapped

149
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

78 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous disruption of this locus results in embryonic lethality.

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All GO Annotations

27
GO References

10

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 differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	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	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	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

675
Tissues

70
cDNA Data

26
Literature Summary

11

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase rbm39

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All Sequences

218
RefSeq

104
UniProt

15
CCDS

CCDS16964.1, CCDS71168.1

Ensembl

ENSMUSG00000027620 (Evidence)
NCBI Gene

170791

			Length	Strain/Species	Flank
genomic	ENSMUSG00000027620	Ensembl Gene Model \| MGI Sequence Detail	33000	C57BL/6J	± kb
transcript	ENSMUST00000109587	Ensembl \| MGI Sequence Detail	2810	Not Applicable
polypeptide	ENSMUSP00000105216	Ensembl \| 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, eukaryotic-type

IPR006509 Splicing factor, RBM39-like

IPR029123 Splicing factor RBM39, linker
GlyGen

Q8VH51 1 site, 1 O-linked glycan (1 site)

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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 60

Developmental Gene Expression 11

Gene Ontology 10

Phenotypes 13
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:326541 Cyagen Biosciences Inc., Cyagen Biosciences Website. 2022;

TSS for Rbm39:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr27044	Chr2:156022055-156022121 (-)	70 bp
Tssr27043	Chr2:156021892-156021903 (-)	260 bp
Tssr27042	Chr2:156019683-156019700 (-)	2,466 bp
Tssr27041	Chr2:156018706-156018738 (-)	3,436 bp
Tssr27040	Chr2:156018491-156018506 (-)	3,659 bp
Tssr27039	Chr2:156016443-156016456 (-)	5,708 bp
Tssr27038	Chr2:156015647-156015651 (-)	6,509 bp
Tssr27037	Chr2:156015096-156015110 (-)	7,055 bp
Tssr27036	Chr2:156014911-156014944 (-)	7,230 bp
Tssr27035	Chr2:156009628-156009674 (-)	12,507 bp
Tssr27034	Chr2:155996214-155996215 (-)	25,943 bp
Tssr27033	Chr2:155994726-155994731 (-)	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, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/01/2026 MGI 6.24