Allc (allantoicase) - Rat Genome Database

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Gene: Allc (allantoicase) Rattus norvegicus
Analyze
Symbol: Allc
Name: allantoicase
RGD ID: 621804
Description: Predicted to enable allantoicase activity. Predicted to be involved in allantoin catabolic process. Orthologous to human ALLC (allantoicase); PARTICIPATES IN purine metabolic pathway; INTERACTS WITH ammonium chloride; bisphenol A; dibutyl phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: allantoate amidinohydrolase; probable allantoicase; probable inactive allantoicase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8650,907,575 - 50,942,665 (-)NCBIGRCr8
mRatBN7.2645,179,181 - 45,214,275 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl645,179,187 - 45,214,223 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx645,470,284 - 45,505,330 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0645,785,148 - 45,820,202 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0645,222,018 - 45,257,066 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0647,812,989 - 47,848,068 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl647,774,060 - 47,848,075 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0656,515,114 - 56,549,982 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4646,421,144 - 46,456,709 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1646,434,446 - 46,444,647 (-)NCBI
Celera644,403,661 - 44,438,351 (-)NCBICelera
Cytogenetic Map6q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Genomic organization and chromosome localization of the murine and human allantoicase gene. Vigetti D, etal., Gene 2002 May 1;289(1-2):13-7.
Additional References at PubMed
PMID:12477932   PMID:14745534   PMID:15489334  


Genomics

Comparative Map Data
Allc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8650,907,575 - 50,942,665 (-)NCBIGRCr8
mRatBN7.2645,179,181 - 45,214,275 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl645,179,187 - 45,214,223 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx645,470,284 - 45,505,330 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0645,785,148 - 45,820,202 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0645,222,018 - 45,257,066 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0647,812,989 - 47,848,068 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl647,774,060 - 47,848,075 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0656,515,114 - 56,549,982 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4646,421,144 - 46,456,709 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1646,434,446 - 46,444,647 (-)NCBI
Celera644,403,661 - 44,438,351 (-)NCBICelera
Cytogenetic Map6q16NCBI
ALLC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3823,645,819 - 3,702,671 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl23,658,200 - 3,702,671 (+)EnsemblGRCh38hg38GRCh38
GRCh3723,705,790 - 3,750,261 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3623,683,661 - 3,728,136 (+)NCBINCBI36Build 36hg18NCBI36
Build 3423,235,579 - 3,243,627NCBI
Celera23,714,865 - 3,759,339 (+)NCBICelera
Cytogenetic Map2p25.3NCBI
HuRef23,647,145 - 3,691,906 (+)NCBIHuRef
CHM1_123,635,517 - 3,679,645 (+)NCBICHM1_1
T2T-CHM13v2.023,668,711 - 3,725,243 (+)NCBIT2T-CHM13v2.0
Allc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391228,603,754 - 28,632,527 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1228,603,754 - 28,632,522 (-)EnsemblGRCm39 Ensembl
GRCm381228,553,755 - 28,582,528 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1228,553,755 - 28,582,523 (-)EnsemblGRCm38mm10GRCm38
MGSCv371229,238,620 - 29,267,348 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361229,140,023 - 29,168,751 (-)NCBIMGSCv36mm8
Celera1230,043,562 - 30,072,354 (-)NCBICelera
Cytogenetic Map12A2NCBI
cM Map1210.97NCBI
Allc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554873,756,789 - 3,774,656 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554873,757,362 - 3,774,067 (-)NCBIChiLan1.0ChiLan1.0
ALLC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212122,801,785 - 122,848,189 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A122,805,762 - 122,852,172 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A3,672,945 - 3,719,340 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A3,591,862 - 3,637,371 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A3,591,862 - 3,637,371 (+)Ensemblpanpan1.1panPan2
ALLC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1172,185,371 - 2,215,256 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl172,185,432 - 2,215,248 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha172,171,942 - 2,201,365 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0172,280,188 - 2,309,631 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl172,280,249 - 2,309,623 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1172,164,986 - 2,194,416 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0172,185,876 - 2,215,277 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0172,187,906 - 2,217,359 (+)NCBIUU_Cfam_GSD_1.0
Allc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629247,027,742 - 47,060,727 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365321,798,884 - 1,815,676 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365321,798,884 - 1,815,666 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ALLC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.13131,195,876 - 131,213,935 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23140,404,710 - 140,422,955 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ALLC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.114103,944,649 - 103,989,845 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl14103,944,761 - 103,975,876 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660458,305,545 - 8,349,837 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Allc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248465,161,153 - 5,170,313 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Allc
247 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:35
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000011048
Prediction methods:Miranda, Rnahybrid
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
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63330954957730294Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63509870971636405Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63569161857730540Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat

Markers in Region
BF387922  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2645,179,256 - 45,179,422 (+)MAPPERmRatBN7.2
Rnor_6.0647,813,064 - 47,813,229NCBIRnor6.0
Rnor_5.0656,515,189 - 56,515,354UniSTSRnor5.0
RGSC_v3.4646,421,215 - 46,421,380UniSTSRGSC3.4
Celera644,403,732 - 44,403,897UniSTS
RH 3.4 Map6260.01UniSTS
Cytogenetic Map6q16UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 7
Low 5 5 5 17 1
Below cutoff 2 6 33 33 2 33 2 3 45 12 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010942   ⟹   ENSRNOP00000010942
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl647,774,060 - 47,811,853 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000011048   ⟹   ENSRNOP00000011048
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl645,179,187 - 45,214,223 (-)Ensembl
Rnor_6.0 Ensembl647,812,994 - 47,848,026 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090017   ⟹   ENSRNOP00000072251
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl647,799,082 - 47,848,075 (-)Ensembl
RefSeq Acc Id: NM_001013037   ⟹   NP_001013055
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8650,907,579 - 50,942,614 (-)NCBI
mRatBN7.2645,179,186 - 45,214,223 (-)NCBI
Rnor_6.0647,812,993 - 47,848,026 (-)NCBI
Rnor_5.0656,515,114 - 56,549,982 (-)NCBI
RGSC_v3.4646,421,144 - 46,456,709 (-)RGD
Celera644,403,661 - 44,438,351 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239944   ⟹   XP_006240006
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8650,907,575 - 50,942,665 (-)NCBI
mRatBN7.2645,179,181 - 45,214,275 (-)NCBI
Rnor_6.0647,812,989 - 47,848,068 (-)NCBI
Rnor_5.0656,515,114 - 56,549,982 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039111788   ⟹   XP_038967716
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8650,907,575 - 50,933,990 (-)NCBI
mRatBN7.2645,179,181 - 45,205,608 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001013055   ⟸   NM_001013037
- UniProtKB: Q8K470 (UniProtKB/Swiss-Prot),   Q6AYP0 (UniProtKB/Swiss-Prot),   A6HB08 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240006   ⟸   XM_006239944
- Peptide Label: isoform X1
- UniProtKB: Q8K470 (UniProtKB/Swiss-Prot),   Q6AYP0 (UniProtKB/Swiss-Prot),   A6HB08 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072251   ⟸   ENSRNOT00000090017
RefSeq Acc Id: ENSRNOP00000010942   ⟸   ENSRNOT00000010942
RefSeq Acc Id: ENSRNOP00000011048   ⟸   ENSRNOT00000011048
RefSeq Acc Id: XP_038967716   ⟸   XM_039111788
- Peptide Label: isoform X2
Protein Domains
Allantoicase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYP0-F1-model_v2 AlphaFold Q6AYP0 1-413 view protein structure

Transcriptome

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

Promoters
RGD ID:13694531
Promoter ID:EPDNEW_R5054
Type:multiple initiation site
Name:Allc_1
Description:allantoicase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5053  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0647,848,057 - 47,848,117EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621804 AgrOrtholog
BioCyc Gene G2FUF-37969 BioCyc
BioCyc Pathway PWY-5697 [allantoin degradation to ureidoglycolate I (urea producing)] BioCyc
BioCyc Pathway Image PWY-5697 BioCyc
Ensembl Genes ENSRNOG00000008299 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011048 ENTREZGENE
  ENSRNOT00000011048.7 UniProtKB/Swiss-Prot
Gene3D-CATH Galactose-binding domain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7111813 IMAGE-MGC_LOAD
InterPro Allantoicase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Allantoicase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Galactose-bd-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:246758 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93851 IMAGE-MGC_LOAD
NCBI Gene 246758 ENTREZGENE
PANTHER ALLANTOICASE UniProtKB/TrEMBL
  ALLANTOICASE-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12045 UniProtKB/Swiss-Prot
Pfam Allantoicase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Allc PhenoGen
PIRSF Allantoicase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008299 RatGTEx
Superfamily-SCOP Galactose-binding domain-like UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6HB08 ENTREZGENE, UniProtKB/TrEMBL
  ALLC_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q8K470 ENTREZGENE
UniProt Secondary Q8K470 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Allc  allantoicase      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Allc  allantoicase      Symbol and Name status set to provisional 70820 PROVISIONAL