Ncln (nicalin) - Rat Genome Database

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Pathways
Gene: Ncln (nicalin) Rattus norvegicus
Analyze
Symbol: Ncln
Name: nicalin
RGD ID: 1309355
Description: Predicted to enable ribosome binding activity. Predicted to be involved in several processes, including multi-pass transmembrane protein insertion into ER membrane; protein stabilization; and regulation of protein complex stability. Predicted to be located in endoplasmic reticulum and membrane. Predicted to be part of multi-pass translocon complex. Predicted to be active in endoplasmic reticulum membrane. Orthologous to human NCLN (nicalin); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BOS complex subunit NCLN; LOC314648; nicalin homolog; nicalin homolog (zebrafish); nicastrin-like protein; RGD1309355; similar to hypothetical protein from EUROIMAGE 2021883
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr878,862,324 - 8,872,699 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl78,862,751 - 8,872,698 (+)EnsemblGRCr8
mRatBN7.278,211,978 - 8,221,938 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,211,996 - 8,221,934 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx711,098,042 - 11,107,974 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0712,973,525 - 12,983,457 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0710,840,645 - 10,850,578 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,081,544 - 11,091,583 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,081,536 - 11,091,584 (+)Ensemblrn6Rnor6.0
Rnor_5.0711,248,733 - 11,258,772 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.479,695,951 - 9,705,989 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera76,402,537 - 6,412,474 (+)NCBICelera
RGSC_v3.179,695,950 - 9,705,988 (+)NCBI
Cytogenetic Map7q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
protein binding  (ISO)
ribosome binding  (IEA,ISO,ISS)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:19946888   PMID:20538592  


Genomics

Comparative Map Data
Ncln
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr878,862,324 - 8,872,699 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl78,862,751 - 8,872,698 (+)EnsemblGRCr8
mRatBN7.278,211,978 - 8,221,938 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,211,996 - 8,221,934 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx711,098,042 - 11,107,974 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0712,973,525 - 12,983,457 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0710,840,645 - 10,850,578 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,081,544 - 11,091,583 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,081,536 - 11,091,584 (+)Ensemblrn6Rnor6.0
Rnor_5.0711,248,733 - 11,258,772 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.479,695,951 - 9,705,989 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera76,402,537 - 6,412,474 (+)NCBICelera
RGSC_v3.179,695,950 - 9,705,988 (+)NCBI
Cytogenetic Map7q11NCBI
NCLN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38193,185,930 - 3,209,575 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl193,185,563 - 3,209,575 (+)Ensemblhg38GRCh38
GRCh37193,185,928 - 3,209,573 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36193,136,875 - 3,160,573 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34193,136,874 - 3,160,572NCBI
Celera193,122,250 - 3,145,978 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef192,952,961 - 2,976,782 (+)NCBIHuRef
CHM1_1193,184,524 - 3,208,222 (+)NCBICHM1_1
T2T-CHM13v2.0193,160,750 - 3,184,441 (+)NCBIT2T-CHM13v2.0
Ncln
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391081,322,289 - 81,333,178 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1081,322,083 - 81,332,226 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381081,486,455 - 81,496,954 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1081,486,249 - 81,496,392 (-)Ensemblmm10GRCm38
MGSCv371080,949,204 - 80,959,108 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361080,889,378 - 80,899,485 (-)NCBIMGSCv36mm8
Celera1082,509,842 - 82,519,746 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Ncln
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554955,222,808 - 5,238,643 (-)Ensembl
ChiLan1.0NW_0049554955,222,990 - 5,238,644 (-)NCBIChiLan1.0ChiLan1.0
NCLN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2207,581,716 - 7,605,672 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1196,815,021 - 6,838,924 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0192,211,474 - 2,235,691 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1193,166,042 - 3,189,681 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl193,166,042 - 3,189,681 (+)EnsemblpanPan2panpan1.1
NCLN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12056,088,017 - 56,104,723 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2056,088,017 - 56,104,723 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2055,811,878 - 55,828,580 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02056,746,690 - 56,763,396 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2056,745,969 - 56,763,411 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12055,802,155 - 55,818,810 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02056,286,144 - 56,302,913 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02056,484,881 - 56,501,641 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ncln
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,994,392 - 216,008,251 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365881,826,045 - 1,840,411 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365881,826,065 - 1,840,391 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCLN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl275,369,955 - 75,390,545 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1275,369,926 - 75,390,609 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2275,891,204 - 75,909,206 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NCLN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.162,948,723 - 2,975,465 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl62,948,212 - 2,975,596 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660815,608,300 - 5,633,124 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ncln
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248286,018,439 - 6,035,446 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248286,018,438 - 6,035,310 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ncln
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11153,392,652 - 153,402,736 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ncln
47 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:159
Count of miRNA genes:107
Interacting mature miRNAs:130
Transcripts:ENSRNOT00000007110
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000007110   ⟹   ENSRNOP00000007110
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl78,862,766 - 8,872,698 (+)Ensembl
mRatBN7.2 Ensembl78,211,996 - 8,221,934 (+)Ensembl
Rnor_6.0 Ensembl711,081,536 - 11,091,584 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000094550   ⟹   ENSRNOP00000077163
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl78,862,751 - 8,872,696 (+)Ensembl
mRatBN7.2 Ensembl78,211,996 - 8,221,934 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000106364   ⟹   ENSRNOP00000088639
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl78,862,751 - 8,872,696 (+)Ensembl
mRatBN7.2 Ensembl78,211,996 - 8,221,934 (+)Ensembl
RefSeq Acc Id: NM_001014082   ⟹   NP_001014104
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr878,862,770 - 8,872,699 (+)NCBI
mRatBN7.278,212,009 - 8,221,938 (+)NCBI
Rnor_6.0711,081,653 - 11,091,582 (+)NCBI
Rnor_5.0711,248,733 - 11,258,772 (+)NCBI
RGSC_v3.479,695,951 - 9,705,989 (+)RGD
Celera76,402,537 - 6,412,474 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240943   ⟹   XP_006241005
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr878,862,324 - 8,872,699 (+)NCBI
mRatBN7.278,211,978 - 8,221,874 (+)NCBI
Rnor_6.0711,081,544 - 11,091,583 (+)NCBI
Rnor_5.0711,248,733 - 11,258,772 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001014104   ⟸   NM_001014082
- Peptide Label: precursor
- UniProtKB: Q5XIA1 (UniProtKB/Swiss-Prot),   A6K875 (UniProtKB/TrEMBL),   A6K876 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241005   ⟸   XM_006240943
- Peptide Label: isoform X1
- UniProtKB: A0A0H2UHD9 (UniProtKB/TrEMBL),   A6K876 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000007110   ⟸   ENSRNOT00000007110
Ensembl Acc Id: ENSRNOP00000077163   ⟸   ENSRNOT00000094550
Ensembl Acc Id: ENSRNOP00000088639   ⟸   ENSRNOT00000106364
Protein Domains
Peptidase M28

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIA1-F1-model_v2 AlphaFold Q5XIA1 1-563 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13694969
Promoter ID:EPDNEW_R5494
Type:initiation region
Name:Ncln_1
Description:nicalin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0711,081,641 - 11,081,701EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309355 AgrOrtholog
BioCyc Gene G2FUF-35036 BioCyc
Ensembl Genes ENSRNOG00000004793 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000094550 ENTREZGENE
Gene3D-CATH Zn peptidases UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7096595 IMAGE-MGC_LOAD
InterPro Nicalin UniProtKB/Swiss-Prot
  Peptidase_M28 UniProtKB/Swiss-Prot
KEGG Report rno:314648 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94760 IMAGE-MGC_LOAD
NCBI Gene 314648 ENTREZGENE
PANTHER PTHR31826 UniProtKB/Swiss-Prot
Pfam Peptidase_M28 UniProtKB/Swiss-Prot
PhenoGen Ncln PhenoGen
PIRSF Nicalin UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000004793 RatGTEx
Superfamily-SCOP Zn-dependent exopeptidases UniProtKB/Swiss-Prot
UniProt A0A0H2UHD9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5YC79_RAT UniProtKB/TrEMBL
  A0A8I6AB62_RAT UniProtKB/TrEMBL
  A6K875 ENTREZGENE, UniProtKB/TrEMBL
  A6K876 ENTREZGENE, UniProtKB/TrEMBL
  NCLN_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Ncln  nicalin  Ncln  nicalin homolog (zebrafish)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ncln  nicalin homolog (zebrafish)  RGD1309355  similar to hypothetical protein from EUROIMAGE 2021883  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1309355  similar to hypothetical protein from EUROIMAGE 2021883  RGD1309355_predicted  similar to hypothetical protein from EUROIMAGE 2021883 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1309355_predicted  similar to hypothetical protein from EUROIMAGE 2021883 (predicted)  LOC314648_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC314648_predicted  similar to hypothetical protein from EUROIMAGE 2021883 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL