Hal (histidine ammonia lyase) - Rat Genome Database

Name: Hal
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Hal (histidine ammonia lyase) Rattus norvegicus

Analyze

Symbol:

Hal

Name:

histidine ammonia lyase

RGD ID:

68363

Description:

Enables histidine ammonia-lyase activity. Predicted to be involved in histidine catabolic process. Predicted to be located in cytoplasm. Human ortholog(s) of this gene implicated in histidinemia. Orthologous to human HAL (histidine ammonia-lyase); PARTICIPATES IN histidine metabolic pathway; histidinemia pathway; INTERACTS WITH (+)-schisandrin B; (R,R,R)-alpha-tocopherol; (S)-colchicine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

histidase; histidine ammonia-lyase

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	HAL (histidine ammonia-lyase)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Hal (histidine ammonia lyase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hal (histidine ammonia-lyase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HAL (histidine ammonia-lyase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HAL (histidine ammonia-lyase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hal (histidine ammonia-lyase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HAL (histidine ammonia-lyase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HAL (histidine ammonia-lyase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hal (histidine ammonia-lyase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	HAL (histidine ammonia-lyase)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Hal (histidine ammonia lyase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hal (histidine ammonia-lyase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	haly-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	hal.1	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	hal.2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	29,894,495 - 29,924,744 (+)	NCBI		GRCr8
mRatBN7.2	7	28,007,449 - 28,037,701 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	28,006,972 - 28,037,701 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	29,997,815 - 30,028,068 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	32,160,030 - 32,190,285 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	31,934,946 - 31,965,140 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	34,326,087 - 34,356,413 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	34,326,087 - 34,356,413 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	34,391,142 - 34,421,405 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	30,520,913 - 30,551,145 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	7	30,541,183 - 30,571,416 (+)	NCBI
Celera	7	25,107,998 - 25,136,986 (+)	NCBI		Celera
RH 3.4 Map	7	191.8	RGD
Cytogenetic Map	7	q13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Experimental Liver Cirrhosis (ISO)

genetic disease (ISO)

histidinemia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(1->4)-beta-D-glucan (ISO)

(R,R,R)-alpha-tocopherol (EXP)

(S)-colchicine (EXP)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (EXP,ISO)

17beta-estradiol (EXP,ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (EXP)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (ISO)

2,4-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

3,3',4,4',5-pentachlorobiphenyl (EXP,ISO)

3,3',5,5'-tetrabromobisphenol A (EXP)

3-chloropropane-1,2-diol (EXP)

4,4'-diaminodiphenylmethane (EXP,ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (EXP)

6-propyl-2-thiouracil (EXP)

7,12-dimethyltetraphene (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

alendronic acid (EXP)

all-trans-retinoic acid (ISO)

amiodarone (EXP)

amitriptyline (EXP)

ammonium chloride (EXP)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenous acid (ISO)

atrazine (EXP)

benzbromarone (EXP)

benzo[a]pyrene (ISO)

beta-naphthoflavone (EXP,ISO)

bisphenol A (EXP)

cadmium dichloride (EXP)

calcitriol (ISO)

cisplatin (ISO)

clofibrate (EXP,ISO)

clofibric acid (EXP)

clomipramine (EXP)

cobalt dichloride (EXP)

corn oil (EXP)

coumarin (EXP)

cyclosporin A (ISO)

cyproconazole (ISO)

dexamethasone (EXP)

diarsenic trioxide (ISO)

dioxygen (ISO)

endosulfan (EXP)

epoxiconazole (ISO)

ethanol (EXP)

etoposide (ISO)

fenofibrate (EXP)

fipronil (EXP)

flutamide (EXP)

fonofos (ISO)

fumonisin B1 (ISO)

gentamycin (EXP)

glafenine (EXP)

gliotoxin (EXP)

graphite (EXP)

hexadecanoic acid (ISO)

imipramine (EXP)

indole-3-methanol (EXP)

indometacin (EXP)

ketoconazole (EXP)

L-ethionine (EXP)

leflunomide (EXP)

metacetamol (ISO)

metformin (EXP)

methapyrilene (EXP)

methoxsalen (ISO)

mono(2-ethylhexyl) phthalate (ISO)

N-nitrosodiethylamine (EXP,ISO)

N-nitrosodimethylamine (EXP)

N-nitrosomorpholine (EXP)

nefazodone (EXP)

nickel atom (ISO)

nimesulide (EXP)

omeprazole (EXP)

orphenadrine (EXP)

paracetamol (EXP,ISO)

parathion (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (EXP,ISO)

perfluorooctanoic acid (EXP,ISO)

phenobarbital (EXP,ISO)

phorbol 13-acetate 12-myristate (ISO)

pinosylvin (ISO)

piperonyl butoxide (EXP)

pirinixic acid (EXP,ISO)

pregnenolone 16alpha-carbonitrile (EXP)

propiconazole (ISO)

quercetin (ISO)

quinolin-8-ol (ISO)

rac-lactic acid (ISO)

raloxifene (EXP)

sanguinarine (ISO)

silicon dioxide (ISO)

sodium arsenate (ISO)

sodium dichromate (EXP)

sotorasib (ISO)

terbufos (ISO)

Tesaglitazar (EXP)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trametinib (ISO)

trans-pinosylvin (ISO)

trichloroethene (ISO)

triphenyl phosphate (EXP)

triptonide (ISO)

tris(2-butoxyethyl) phosphate (ISO)

troglitazone (EXP,ISO)

urethane (ISO)

valproic acid (ISO)

vanadyl sulfate (ISO)

vinclozolin (EXP)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

histidine catabolic process (IBA,ISO)

histidine catabolic process to glutamate and formamide (IEA)

histidine catabolic process to glutamate and formate (IEA)

histidine metabolic process (TAS)

Cellular Component

cytoplasm (IEA)

Molecular Function

histidine ammonia-lyase activity (IBA,IDA,ISO,TAS)

Molecular Pathway Annotations Click to see Annotation Detail View

histidine metabolic pathway (IEA,ISO)

histidinemia pathway (ISO)

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.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	KEGG: Kyoto Encyclopedia of Genes and Genomes	KEGG
4.	High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence.	Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
5.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
7.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
8.	SMPDB Annotation Import Pipeline	Pipeline to import SMPDB annotations from SMPDB into RGD
9.	GOA pipeline	RGD automated data pipeline
10.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
12.	Isolation of a rat histidase cDNA sequence and expression in Escherichia coli--evidence of extrahepatic/epidermal distribution.	Sano H, etal., Eur J Biochem 1997 Nov 15;250(1):212-21.
13.	Cloning and expression of rat histidase. Homology to two bacterial histidases and four phenylalanine ammonia-lyases.	Taylor RG, etal., J Biol Chem 1990 Oct 25;265(30):18192-9.
14.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
15.	Soy protein, casein, and zein regulate histidase gene expression by modulating serum glucagon.	Tovar AR, etal., Am J Physiol Endocrinol Metab 2002 Nov;283(5):E1016-22.

Additional References at PubMed

PMID:7961661	PMID:8486363	PMID:12477932	PMID:15741241	PMID:15806399

Genomics

Comparative Map Data

Hal
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	29,894,495 - 29,924,744 (+)	NCBI		GRCr8
mRatBN7.2	7	28,007,449 - 28,037,701 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	28,006,972 - 28,037,701 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	29,997,815 - 30,028,068 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	32,160,030 - 32,190,285 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	31,934,946 - 31,965,140 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	34,326,087 - 34,356,413 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	34,326,087 - 34,356,413 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	34,391,142 - 34,421,405 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	30,520,913 - 30,551,145 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	7	30,541,183 - 30,571,416 (+)	NCBI
Celera	7	25,107,998 - 25,136,986 (+)	NCBI		Celera
RH 3.4 Map	7	191.8	RGD
Cytogenetic Map	7	q13	NCBI

HAL
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	95,972,662 - 95,996,344 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	95,972,662 - 95,996,365 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	96,366,440 - 96,390,122 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	94,891,273 - 94,914,202 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	94,869,609 - 94,892,539	NCBI
Celera	12	96,033,432 - 96,056,362 (-)	NCBI		Celera
Cytogenetic Map	12	q23.1	NCBI
HuRef	12	93,428,306 - 93,452,016 (-)	NCBI		HuRef
CHM1_1	12	96,331,432 - 96,355,134 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	12	95,946,669 - 95,970,341 (-)	NCBI		T2T-CHM13v2.0

Hal
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	93,324,630 - 93,352,623 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	10	93,324,630 - 93,355,166 (+)	Ensembl		GRCm39 Ensembl
GRCm38	10	93,488,768 - 93,516,761 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	93,488,768 - 93,519,304 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	92,951,513 - 92,979,488 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	10	93,707,053 - 93,735,128 (+)	NCBI		MGSCv36	mm8
MGSCv36	10	92,918,567 - 92,946,542 (+)	NCBI		MGSCv36	mm8
Celera	10	95,474,543 - 95,502,727 (+)	NCBI		Celera
Cytogenetic Map	10	C2	NCBI
cM Map	10	48.49	NCBI

Hal
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955405	32,316,326 - 32,341,485 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955405	32,317,345 - 32,341,409 (-)	NCBI	ChiLan1.0	ChiLan1.0

HAL
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	10	104,043,373 - 104,067,070 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	104,039,763 - 104,063,460 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	93,561,401 - 93,585,215 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	96,950,020 - 96,973,662 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	96,950,020 - 96,973,662 (-)	Ensembl	panpan1.1		panPan2

HAL
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	15	35,767,314 - 35,791,086 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	15	35,759,672 - 35,791,003 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	15	36,153,957 - 36,177,503 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	15	36,432,429 - 36,455,977 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	15	36,433,070 - 36,455,953 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	15	35,705,313 - 35,728,861 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	15	35,799,841 - 35,823,389 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	15	36,063,032 - 36,086,577 (-)	NCBI		UU_Cfam_GSD_1.0

Hal
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	24,156,940 - 24,178,046 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936507	12,058,698 - 12,078,214 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936507	12,058,583 - 12,078,159 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HAL
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	87,522,542 - 87,547,455 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	87,522,483 - 87,547,489 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	91,725,402 - 91,751,694 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HAL
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	11	91,343,715 - 91,367,384 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666037	153,758,865 - 153,784,917 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hal
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624750	11,318,511 - 11,343,459 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624750	11,318,572 - 11,344,326 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Hal
179 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	83
Count of miRNA genes:	75
Interacting mature miRNAs:	80
Transcripts:	ENSRNOT00000006971
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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
7411566	Bw136	Body weight QTL 136	10.4	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	7	1	31962314	Rat
9590142	Scort5	Serum corticosterone level QTL 5	24.4	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	7	1	31962314	Rat
724560	Plsm3	Polydactyly-luxate syndrome (PLS) morphotypes QTL 3		0.0003	tibia length (VT:0004357)	tibia length (CMO:0000450)	7	1	34000259	Rat
2317047	Wbc4	White blood cell count QTL 4		0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	7	1	35342956	Rat
61410	Bw19	Body weight QTL 19	6.2	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	7	1	44782185	Rat
631503	Bp102	Blood pressure QTL 102	1.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	1	44822433	Rat
634336	Anxrr17	Anxiety related response QTL 17	3.66		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	7	924703	115097879	Rat
10755438	Coatc9	Coat color QTL 9		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	3529280	48529280	Rat
9590102	Sffal5	Serum free fatty acids level QTL 5	8.62	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	7	5329019	50329019	Rat
10755440	Coatc10	Coat color QTL 10		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	7496499	52496499	Rat
10059592	Kidm45	Kidney mass QTL 45	3.95	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	7	7573985	52573985	Rat
2298547	Neuinf5	Neuroinflammation QTL 5	3.7		nervous system integrity trait (VT:0010566)	spinal cord Cd74 protein level (CMO:0002131)	7	9462246	58265113	Rat
1643004	Pain2	Pain QTL 2	1		mechanical nociception trait (VT:0002734)	self mutilation severity score (CMO:0002145)	7	9462246	98011544	Rat
1578652	Bmd15	Bone mineral density QTL 15	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	7	9866467	60460686	Rat
738033	Anxrr6	Anxiety related response QTL 6	4.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	7	15573889	60573889	Rat
1582260	Bw72	Body weight QTL 72	3.2	0.0043	body mass (VT:0001259)	body weight (CMO:0000012)	7	15795565	38073970	Rat
1582261	Bw69	Body weight QTL 69	3.2	0.0048	body mass (VT:0001259)	body weight (CMO:0000012)	7	15795565	38073970	Rat
1582262	Bw75	Body weight QTL 75	3	0.0038	body mass (VT:0001259)	body weight (CMO:0000012)	7	15795565	38073970	Rat
2317059	Aia15	Adjuvant induced arthritis QTL 15	2.46		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	7	17004598	62004598	Rat
10755451	Coatc11	Coat color QTL 11		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	17944357	62944357	Rat
61369	Mcs2	Mammary carcinoma susceptibility QTL 2	3.38		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	7	19032807	35526300	Rat
1354637	Scl30	Serum cholesterol level QTL 30	3.7		blood cholesterol amount (VT:0000180)	blood total cholesterol level (CMO:0000051)	7	19654317	49753746	Rat
1354644	Spl4	Serum phospholipid level QTL 4	4.9		blood phospholipid amount (VT:0006084)	blood phospholipid level (CMO:0001169)	7	19654317	49753746	Rat
1354639	Spl5	Serum phospholipid level QTL 5	3.9		blood LDL phospholipid amount (VT:0010505)	blood low density lipoprotein phospholipid level (CMO:0001568)	7	19654317	52888450	Rat
1300132	Bp182	Blood pressure QTL 182	3.49		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	7	19654317	84928080	Rat
2290372	Gluco33	Glucose level QTL 33	2.71		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	7	20555705	29891047	Rat
7411569	Bw137	Body weight QTL 137		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	7	21921195	66921195	Rat
1641885	Alcrsp9	Alcohol response QTL 9			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	7	24099606	69099606	Rat
1549840	Bss5	Bone structure and strength QTL 5	9.8		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	7	24751841	69751841	Rat
70190	Mcs6	Mammary carcinoma susceptibility QTL 6	2.29		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	7	26737401	63902784	Rat

Markers in Region

RH142423

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	28,021,944 - 28,022,212 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	34,340,581 - 34,340,848	NCBI	Rnor6.0
Rnor_5.0	7	34,405,636 - 34,405,903	UniSTS	Rnor5.0
RGSC_v3.4	7	30,535,407 - 30,535,674	UniSTS	RGSC3.4
Celera	7	25,122,491 - 25,122,758	UniSTS
RH 3.4 Map	7	191.8	UniSTS
Cytogenetic Map	7	q13	UniSTS

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

	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		23	23		23
Low		18	18		18			3		10	1
Below cutoff	1	14		11		4	5	20	8	19	7	4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017159	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB002393	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB002394	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC089809	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473960	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000007	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M58308	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000006971 ⟹ ENSRNOP00000006971

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	7	28,006,972 - 28,037,701 (+)	Ensembl
Rnor_6.0 Ensembl	7	34,326,087 - 34,356,413 (+)	Ensembl

RefSeq Acc Id:

NM_017159 ⟹ NP_058855

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	7	29,894,495 - 29,924,744 (+)	NCBI
mRatBN7.2	7	28,007,449 - 28,037,701 (+)	NCBI
Rnor_6.0	7	34,326,087 - 34,356,413 (+)	NCBI
Rnor_5.0	7	34,391,142 - 34,421,405 (+)	NCBI
RGSC_v3.4	7	30,520,913 - 30,551,145 (+)	RGD
Celera	7	25,107,998 - 25,136,986 (+)	RGD

Sequence:

show sequence

GGTGAGCCATGCCTAGGTACACGGTGCACGTGCGTGGGGAATGGCTGGCGGTACCCTGCCAGGA
CGGGAAGCTCAGTGTTGGCTGGCTGGGCCGCGAGGCTGTGCGGCGCTACATGAAGAACAAGCCG
GACAACGGGGGCTTCACCTCGGTGGATGAAGTGCGATTCCTTGTGCGCCGGTGCAAGGGCCTGG
GCCTGTTGGACAATGAGGACCTGCTGGAGGTGGCCCTGGAGGACAATGAGTTCGTAGAAGTGGT
GATTGAAGGCGATGTAATGTCTCCTGATTTCATTCCATCACAGCCAGAAGGCGTTTTCCTTTAC
AGCAAATACCGGGAGCCTGAAAAGTACATTGCCTTGGATGGGGACAGTCTGAGCACGGAGGATC
TGGTCAACCTAGGCAAGGGACATTACAAGATAAAGCTCACTTCAATAGCTGAGAAGAAAGTGCA
GCAGTCCCGGGAAGTCATTGACAGCATCATAAAAGAAAGAACAGTTGTTTACGGCATCACCACG
GGTTTTGGAAAATTTGCCAGAACTGTGATCCCTGCCAATAAGCTACAGGAGCTTCAGGTCAACT
TAGTCCGTTCCCATTCTTCAGGTGTTGGGAAGCCACTCAGTCCTGAGAGGTGTCGGATGCTCTT
GGCTTTGAGGATCAATGTCTTAGCCAAAGGATACAGTGGGATTTCCTTGGAGACCCTGAAACAA
GTGATTGAAGTATTTAATGCCTCCTGCCTGTCCTATGTTCCAGAGAAAGGGACCGTTGGTGCCA
GCGGAGACCTTGCCCCACTCTCCCATCTTGCTTTGGGGCTCATTGGAGAAGGAAAGATGTGGTC
CCCAAAGAGTGGCTGGGCCGATGCCAAATATGTCTTAGAAGCCCACGGATTGAAACCAATTGTT
CTGAAACCAAAAGAAGGCCTGGCACTCATCAACGGGACACAGATGATCACTTCCCTGGGCTGTG
AAGCCGTGGAGCGAGCCAGCGCCATTGCCCGGCAAGCGGATATCGTGGCTGCCTTGACCCTCGA
GGTGCTGAAGGGCACCACCAAAGCCTTCGATACCGACATCCACGCCGTCCGCCCTCACCGCGGG
CAAATTGAAGTTGCTTTCCGGTTCCGGTCCCTCTTGGACTCAGATCACCACCCGTCAGAAATTG
CAGAAAGCCACAGGTTCTGTGATCGTGTTCAGGATGCGTACACCTTACGCTGCTGTCCACAGGT
CCACGGTGTGGTGAACGATACAATTGCCTTTGTGAAGGACATCATCACCACAGAACTGAACAGT
GCCACAGACAATCCTATGGTCTTTGCCAGTCGAGGGGAGACAATTTCGGGAGGAAACTTCCACG
GTGAATACCCAGCCAAAGCCCTGGACTATTTGGCCATTGGCGTCCATGAACTTGCGGCAATTAG
TGAAAGAAGAATCGAAAGGCTGTGTAATCCTTCCCTCAGTGAGCTGCCCGCCTTCCTGGTGGCT
GAAGGAGGTCTCAATTCTGGATTCATGATAGCCCACTGTACCGCAGCAGCCCTGGTGTCTGAGA
GCAAGGCTCTGTGCCACCCTTCATCTGTGGACTCACTCTCTACCAGTGCTGCCACGGAGGACCA
CGTCTCCATGGGAGGATGGGCAGCCAGGAAAGCTCTCAGGGTCATCGAGCACGTGGAACAAGTG
CTGGCCATTGAGCTTCTCGCGGCCTGCCAGGGCATAGAGTTTCTGCGCCCCTTGAAAACAACCA
CTCCGCTGGAGAAGGTGTACGACCTGGTGCGCTCCGTAGTAAGGCCCTGGATCAAAGATCGCTT
CATGGCCCCGGACATCGAGGCAGCACACAGGTTGCTTCTTGACCAGAAGGTTTGGGAGGTGGCT
GCCCCGTACATCGAGAAATACAGAATGGAGCACATTCCGGAATCCAGACCGCTTTCTCCAACAG
CGTTTTCACTAGAATCTCTGAGGAAGAATTCAGCCACAATCCCAGAGTCTGACGATCTTTAACG
GGCTTCCTCGAGAACAGGCACATGTGTCGGATCTGGGCACATCACTGGTGTGGTGACGGAGAGT
CTCAGGAACCGCCCATGATGTGTAGAACTCATCTCTTTTCAAACAAACTCTGGTTAAATCATGG
CAGCAATACAGTCATTGAACCCAG

hide sequence

Protein Sequences


Protein RefSeqs	NP_058855	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA63491	(Get FASTA)	NCBI Sequence Viewer
	AAH89809	(Get FASTA)	NCBI Sequence Viewer
	BAA24432	(Get FASTA)	NCBI Sequence Viewer
	BAA24433	(Get FASTA)	NCBI Sequence Viewer
	EDM16911	(Get FASTA)	NCBI Sequence Viewer
	EDM16912	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000006971
	ENSRNOP00000006971.4
	ENSRNOP00055007321
	ENSRNOP00060039850
	ENSRNOP00065015276
GenBank Protein	P21213	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_058855 ⟸ NM_017159

- UniProtKB:

Q5EBB8 (UniProtKB/Swiss-Prot), P21213 (UniProtKB/Swiss-Prot), A6IFY6 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPRYTVHVRGEWLAVPCQDGKLSVGWLGREAVRRYMKNKPDNGGFTSVDEVRFLVRRCKGLGLL
DNEDLLEVALEDNEFVEVVIEGDVMSPDFIPSQPEGVFLYSKYREPEKYIALDGDSLSTEDLVN
LGKGHYKIKLTSIAEKKVQQSREVIDSIIKERTVVYGITTGFGKFARTVIPANKLQELQVNLVR
SHSSGVGKPLSPERCRMLLALRINVLAKGYSGISLETLKQVIEVFNASCLSYVPEKGTVGASGD
LAPLSHLALGLIGEGKMWSPKSGWADAKYVLEAHGLKPIVLKPKEGLALINGTQMITSLGCEAV
ERASAIARQADIVAALTLEVLKGTTKAFDTDIHAVRPHRGQIEVAFRFRSLLDSDHHPSEIAES
HRFCDRVQDAYTLRCCPQVHGVVNDTIAFVKDIITTELNSATDNPMVFASRGETISGGNFHGEY
PAKALDYLAIGVHELAAISERRIERLCNPSLSELPAFLVAEGGLNSGFMIAHCTAAALVSESKA
LCHPSSVDSLSTSAATEDHVSMGGWAARKALRVIEHVEQVLAIELLAACQGIEFLRPLKTTTPL
EKVYDLVRSVVRPWIKDRFMAPDIEAAHRLLLDQKVWEVAAPYIEKYRMEHIPESRPLSPTAFS
LESLRKNSATIPESDDL

hide sequence

RefSeq Acc Id:

ENSRNOP00000006971 ⟸ ENSRNOT00000006971

Protein Domains

Par3/HAL N-terminal

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P21213-F1-model_v2	AlphaFold	P21213	1-657	view protein structure

Transcriptome

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

Promoters

RGD ID:

13695146

Promoter ID:

EPDNEW_R5671

Type:

multiple initiation site

Name:

Hal_1

Description:

histidine ammonia lyase

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	7	34,326,031 - 34,326,091	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:68363	AgrOrtholog
BioCyc Gene	G2FUF-34389	BioCyc
BioCyc Pathway	HISHP-PWY [L-histidine degradation VI]	BioCyc
	PWY-5030 [L-histidine degradation III]	BioCyc
BioCyc Pathway Image	HISHP-PWY	BioCyc
	PWY-5030	BioCyc
Ensembl Genes	ENSRNOG00000004502	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOG00055005880	UniProtKB/Swiss-Prot
	ENSRNOG00060027612	UniProtKB/Swiss-Prot
	ENSRNOG00065012257	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000006971	ENTREZGENE
	ENSRNOT00000006971.7	UniProtKB/Swiss-Prot
	ENSRNOT00055009508	UniProtKB/Swiss-Prot
	ENSRNOT00060047906	UniProtKB/Swiss-Prot
	ENSRNOT00065019927	UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.275.10	UniProtKB/Swiss-Prot
	Fumarase/aspartase (Central domain)	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Fumarase/aspartase (N-terminal domain)	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7325816	IMAGE-MGC_LOAD
InterPro	Aromatic_Lyase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Fumarase/histidase_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HutH	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	L-Aspartase-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Par3/HAL_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Phe/His_NH3-lyase_AS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:29301	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:108720	IMAGE-MGC_LOAD
NCBI Gene	29301	ENTREZGENE
PANTHER	HISTIDINE AMMONIA-LYASE	UniProtKB/Swiss-Prot
	HISTIDINE AMMONIA-LYASE	UniProtKB/TrEMBL
	HISTIDINE AMMONIA-LYASE	UniProtKB/TrEMBL
	PTHR10362	UniProtKB/Swiss-Prot
Pfam	Lyase_aromatic	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Par3_HAL_N_term	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Hal	PhenoGen
PROSITE	PAL_HISTIDASE	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000004502	RatGTEx
	ENSRNOG00055005880	RatGTEx
	ENSRNOG00060027612	RatGTEx
	ENSRNOG00065012257	RatGTEx
Superfamily-SCOP	L-aspartase-like	UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
TIGR	TC233953
UniProt	A6IFY6	ENTREZGENE, UniProtKB/TrEMBL
	A6IFY7_RAT	UniProtKB/TrEMBL
	HUTH_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q5EBB8	ENTREZGENE
UniProt Secondary	Q5EBB8	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2002-06-10	Hal	histidine ammonia lyase			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_cellular_localization	localized to the cytosol	632935
gene_expression	expressed in liver, skin, renal cortex tubular epithelium, fundic mucosal glands of stomach, gastric intramuscular (Auerbach's) plexus, and adrenal cortex	632935
gene_expression	expressed in liver and skin	628345
gene_function	catalyzes the oxidative deamination of histidine to form urocanic acid	628345
gene_process	catabolizes and thereby eliminates excess histidine in liver	628345
gene_regulation	enzyme activity is increased by casein, soy or zein diets and is correlated with serum concentrations of glucagon	628345
gene_regulation	mRNA in the liver is regulated by the dietary protein content	628345

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

BioCyc Pathways

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

BioCyc Pathways