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Calu calumenin [ Rattus norvegicus (Norway rat) ]

Gene ID: 64366, updated on 8-Oct-2019

Summary

Official Symbol
Caluprovided by RGD
Official Full Name
calumeninprovided by RGD
Primary source
RGD:620383
See related
Ensembl:ENSRNOG00000006197
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Rcn; Cbp50
Summary
binds calcium; localized to the endoplasmic reticulum lumen [RGD, Feb 2006]
Expression
Biased expression in Heart (RPKM 931.3), Lung (RPKM 569.4) and 9 other tissues See more
Orthologs

Genomic context

See Calu in Genome Data Viewer
Location:
4q22
Exon count:
8
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (56625611..56653112)
106 current Rn_Celera (GCF_000002265.2) 4 AC_000072.1 (53057097..53084601)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 4 NC_005103.3 (56392772..56420273)

Chromosome 4 - NC_005103.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC103692085 Neighboring gene family with sequence similarity 71, member F2 Neighboring gene family with sequence similarity 71, member F1 Neighboring gene opsin 1, short wave sensitive Neighboring gene transfer RNA proline (anticodon AGG)

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

General gene information

Markers

Homology

Clone Names

  • MGC124555

Gene Ontology Provided by RGD

Function Evidence Code Pubs
calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
calcium ion binding ISO
Inferred from Sequence Orthology
more info
PubMed 
enzyme binding IDA
Inferred from Direct Assay
more info
PubMed 
enzyme inhibitor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
negative regulation of catalytic activity IEA
Inferred from Electronic Annotation
more info
 
peripheral nervous system axon regeneration IEP
Inferred from Expression Pattern
more info
PubMed 
response to organic cyclic compound IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
PubMed 
endoplasmic reticulum lumen IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
PubMed 
melanosome IEA
Inferred from Electronic Annotation
more info
 
sarcoplasmic reticulum lumen IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
calumenin
Names
CBP-50
crocalbin
reticulocalbin

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001033898.1NP_001029070.1  calumenin isoform b precursor

    See identical proteins and their annotated locations for NP_001029070.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks one alternate in-frame exon and contains another alternate in-frame exon compare to variant 1. The resulting isoform (b) is of the same size as isoform a, but it differs in its internal aa sequence.
    Source sequence(s)
    BC101908
    UniProtKB/TrEMBL
    Q3MID6
    Related
    ENSRNOP00000008972.4, ENSRNOT00000008972.6
    Conserved Domains (3) summary
    cd00051
    Location:157214
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam13499
    Location:157214
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:193258
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
  2. NM_022535.2NP_071980.2  calumenin isoform a precursor

    See identical proteins and their annotated locations for NP_071980.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform a. Both isoforms are of the same length but differ in their internal aa sequence.
    Source sequence(s)
    BC101908, CK476875
    UniProtKB/TrEMBL
    G3V6S3, Q3MID6
    Related
    ENSRNOP00000008356.3, ENSRNOT00000008356.5
    Conserved Domains (3) summary
    cd00051
    Location:157214
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam13499
    Location:157214
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:193258
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005103.4 Reference Rnor_6.0 Primary Assembly

    Range
    56625611..56653112
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Rn_Celera

Genomic

  1. AC_000072.1 Alternate Rn_Celera

    Range
    53057097..53084601
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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