Hmcn2 (hemicentin 2) - Rat Genome Database

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Gene: Hmcn2 (hemicentin 2) Rattus norvegicus
Analyze
Symbol: Hmcn2
Name: hemicentin 2
RGD ID: 1585467
Description: Predicted to enable calcium ion binding activity. Predicted to be located in several cellular components, including basement membrane; cell cortex; and extracellular region. Orthologous to human HMCN2 (hemicentin 2); INTERACTS WITH atrazine; bisphenol A; manganese(II) chloride.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: hemicentin-2; LOC311858; LOC686132; LOC688582; similar to hemicentin 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8334,986,246 - 35,136,047 (+)NCBIGRCr8
mRatBN7.2314,588,353 - 14,738,320 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl314,588,662 - 14,738,025 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0310,384,873 - 10,536,529 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0315,744,235 - 15,895,200 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4310,539,893 - 10,565,034 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera39,344,250 - 9,492,987 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17015624   PMID:27068509  


Genomics

Comparative Map Data
Hmcn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8334,986,246 - 35,136,047 (+)NCBIGRCr8
mRatBN7.2314,588,353 - 14,738,320 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl314,588,662 - 14,738,025 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0310,384,873 - 10,536,529 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0315,744,235 - 15,895,200 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4310,539,893 - 10,565,034 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera39,344,250 - 9,492,987 (+)NCBICelera
Cytogenetic Map3p12NCBI
HMCN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389130,265,760 - 130,434,123 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9130,265,760 - 130,434,123 (+)EnsemblGRCh38hg38GRCh38
GRCh379133,028,039 - 133,309,510 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369132,213,210 - 132,299,331 (+)NCBINCBI36Build 36hg18NCBI36
Celera9103,680,254 - 103,847,667 (+)NCBICelera
Cytogenetic Map9q34.11NCBI
HuRef9102,727,648 - 102,795,339 (+)NCBIHuRef
CHM1_19133,372,532 - 133,458,435 (+)NCBICHM1_1
T2T-CHM13v2.09142,470,624 - 142,639,100 (+)NCBIT2T-CHM13v2.0
Hmcn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39231,204,273 - 31,350,751 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl231,204,427 - 31,350,750 (+)EnsemblGRCm39 Ensembl
GRCm38231,314,255 - 31,460,738 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl231,314,415 - 31,460,738 (+)EnsemblGRCm38mm10GRCm38
MGSCv37231,169,935 - 31,316,258 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36231,202,212 - 31,258,721 (+)NCBIMGSCv36mm8
Celera231,081,120 - 31,161,655 (+)NCBICelera
Cytogenetic Map2BNCBI
cM Map221.81NCBI
Hmcn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955513303,490 - 434,207 (+)NCBIChiLan1.0ChiLan1.0
HMCN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2118,917,714 - 9,082,943 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan198,920,062 - 9,085,287 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09101,393,336 - 101,558,733 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19130,044,736 - 130,209,217 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9130,044,739 - 130,208,799 (+)Ensemblpanpan1.1panPan2
HMCN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1953,486,151 - 53,633,340 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl953,485,760 - 53,633,808 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha952,681,724 - 52,829,027 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0954,382,674 - 54,530,365 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl954,456,780 - 54,530,814 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1953,160,087 - 53,307,383 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0953,481,246 - 53,628,642 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0953,573,838 - 53,720,749 (-)NCBIUU_Cfam_GSD_1.0
Hmcn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947197,581,628 - 197,702,992 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493648717,350,511 - 17,471,506 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMCN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1270,363,978 - 270,523,262 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11270,364,005 - 270,522,977 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21304,331,043 - 304,445,872 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HMCN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1127,710,822 - 7,881,086 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660797,570,244 - 7,748,515 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hmcn2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247605,229,490 - 5,356,655 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247605,229,200 - 5,356,655 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hmcn2
1063 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:61
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000011676
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)31043430624512004Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat

Markers in Region
D3Cebr2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2314,647,135 - 14,647,334 (-)MAPPERmRatBN7.2
Rnor_6.0310,477,004 - 10,477,202NCBIRnor6.0
Rnor_5.0315,836,366 - 15,836,564UniSTSRnor5.0
RGSC_v3.4310,434,751 - 10,434,949UniSTSRGSC3.4
Celera39,402,649 - 9,402,847UniSTS
Cytogenetic Map3p12UniSTS
RH133210  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2314,738,082 - 14,738,296 (-)MAPPERmRatBN7.2
Rnor_6.0310,384,896 - 10,385,109NCBIRnor6.0
Rnor_5.0315,744,258 - 15,744,471UniSTSRnor5.0
RGSC_v3.4310,564,798 - 10,565,011UniSTSRGSC3.4
Celera39,492,751 - 9,492,964UniSTS
RH 3.4 Map351.0UniSTS
Cytogenetic Map3p12UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSRNOT00000111278   ⟹   ENSRNOP00000080634
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl314,588,662 - 14,738,025 (+)Ensembl
RefSeq Acc Id: XM_039106171   ⟹   XP_038962099
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8334,986,246 - 35,136,047 (+)NCBI
mRatBN7.2314,588,737 - 14,738,320 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038962099 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93274 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000080634.1
RefSeq Acc Id: XP_038962099   ⟸   XM_039106171
- UniProtKB: A0A8I5ZQ55 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000080634   ⟸   ENSRNOT00000111278
Protein Domains
EGF-like   Ig-like   Nidogen G2 beta-barrel

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1585467 AgrOrtholog
BioCyc Gene G2FUF-50179 BioCyc
Ensembl Genes ENSRNOG00000064166 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000111278.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.155.10 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
  Laminin UniProtKB/TrEMBL
InterPro cEGF UniProtKB/TrEMBL
  Cell_Adh-Cytoskel_Orgn UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/TrEMBL
  G2_nidogen/fibulin_G2F UniProtKB/TrEMBL
  GFP UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_I-set UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  NOTCH1_EGF-like UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene 686132 ENTREZGENE
PANTHER CONTACTIN 5 UniProtKB/TrEMBL
  HEMICENTIN-2-RELATED UniProtKB/TrEMBL
Pfam cEGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  G2F UniProtKB/TrEMBL
  I-set UniProtKB/TrEMBL
  Ig_3 UniProtKB/TrEMBL
PhenoGen Hmcn2 PhenoGen
PROSITE ASX_HYDROXYL UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  IG_LIKE UniProtKB/TrEMBL
  NIDOGEN_G2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000064166 RatGTEx
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  G2F UniProtKB/TrEMBL
  IGc2 UniProtKB/TrEMBL
  IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
  SSF54511 UniProtKB/TrEMBL
  SSF57184 UniProtKB/TrEMBL
UniProt A0A8I5ZQ55 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Hmcn2  hemicentin 2  Hmcn2  hemicentin 2  Data merged from RGD:149736432 737654 PROVISIONAL
2021-08-09 Hmcn2  hemicentin 2      Symbol and Name status set to provisional 45752 PROVISIONAL
2015-07-29 Hmcn2  hemicentin 2  LOC688582  similar to hemicentin 1  Data merged from RGD:1587597 737654 PROVISIONAL
2008-03-05 Hmcn2  hemicentin 2  LOC686132  similar to hemicentin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC686132  similar to hemicentin 1  LOC687117  similar to hemicentin 1  Data merged from RGD:1588969 1643240 APPROVED
2008-01-09 LOC688582  similar to hemicentin 1  RGD1565958_predicted  similar to hypothetical protein (predicted)  Data merged from RGD:1565958 1643240 APPROVED
2006-11-19 LOC688582  similar to hemicentin 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC686132  similar to hemicentin 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687117  similar to hemicentin 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1565958_predicted  similar to hypothetical protein (predicted)  LOC311858  similar to hypothetical protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC311858  similar to hypothetical protein      Symbol and Name status set to provisional 70820 PROVISIONAL