Scgb3a1 (secretoglobin, family 3A, member 1) - Rat Genome Database

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Gene: Scgb3a1 (secretoglobin, family 3A, member 1) Rattus norvegicus
Analyze
Symbol: Scgb3a1
Name: secretoglobin, family 3A, member 1
RGD ID: 727901
Description: Predicted to be involved in positive regulation of myoblast fusion. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human SCGB3A1 (secretoglobin family 3A member 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Hin1; pneumo secretory protein 2; PnSP-2; Pnsp2; secretoglobin; secretoglobin family 3A member 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
mRatBN7.21033,968,059 - 33,969,366 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1033,968,059 - 33,969,476 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1038,643,651 - 38,644,958 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0107,182,054 - 7,183,361 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01033,637,313 - 33,638,620 (+)NCBIRnor_WKY
Rnor_6.01035,133,561 - 35,134,868 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1035,133,252 - 35,135,466 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01034,905,080 - 34,906,387 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41035,125,569 - 35,126,876 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11035,127,288 - 35,128,035 (+)NCBI
Celera1033,324,580 - 33,325,887 (+)NCBICelera
Cytogenetic Map10q21NCBI
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

Biological Process

Cellular Component

Molecular Function

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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
4. Secretoglobins SCGB3A1 and SCGB3A2 define secretory cell subsets in mouse and human airways. Reynolds SD, etal., Am J Respir Crit Care Med 2002 Dec 1;166(11):1498-509. Epub 2002 Aug 1.
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11481438   PMID:16502470   PMID:19199708   PMID:23844157  


Genomics

Comparative Map Data
Scgb3a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21033,968,059 - 33,969,366 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1033,968,059 - 33,969,476 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1038,643,651 - 38,644,958 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0107,182,054 - 7,183,361 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01033,637,313 - 33,638,620 (+)NCBIRnor_WKY
Rnor_6.01035,133,561 - 35,134,868 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1035,133,252 - 35,135,466 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01034,905,080 - 34,906,387 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41035,125,569 - 35,126,876 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11035,127,288 - 35,128,035 (+)NCBI
Celera1033,324,580 - 33,325,887 (+)NCBICelera
Cytogenetic Map10q21NCBI
SCGB3A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385180,590,105 - 180,591,499 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl5180,590,105 - 180,591,499 (-)EnsemblGRCh38hg38GRCh38
GRCh375180,017,105 - 180,018,499 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365179,949,711 - 179,951,093 (-)NCBINCBI36Build 36hg18NCBI36
Build 345179,949,711 - 179,951,093NCBI
Celera5175,639,688 - 175,641,070 (-)NCBICelera
Cytogenetic Map5q35.3NCBI
HuRef5174,741,080 - 174,742,462 (-)NCBIHuRef
CHM1_15179,449,540 - 179,450,922 (-)NCBICHM1_1
T2T-CHM13v2.05181,145,993 - 181,147,387 (-)NCBIT2T-CHM13v2.0
Scgb3a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391149,554,422 - 49,555,945 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1149,554,437 - 49,555,945 (+)EnsemblGRCm39 Ensembl
GRCm381149,663,595 - 49,665,118 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1149,663,610 - 49,665,118 (+)EnsemblGRCm38mm10GRCm38
MGSCv371149,477,112 - 49,478,620 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361149,507,033 - 49,508,541 (+)NCBIMGSCv36mm8
Celera1154,225,407 - 54,226,915 (+)NCBICelera
Cytogenetic Map11B1.2NCBI
cM Map1129.75NCBI
Scgb3a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955408147,777 - 149,227 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955408147,777 - 149,227 (+)NCBIChiLan1.0ChiLan1.0
SCGB3A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v05175,792,429 - 175,797,122 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
Scgb3a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213119,092,049 - 119,093,637 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936739300,579 - 303,414 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCGB3A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl278,125,825 - 78,127,793 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1278,125,874 - 78,127,791 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2279,514,776 - 79,560,816 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SCGB3A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12382,315,106 - 82,317,600 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607513,735,739 - 13,737,333 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scgb3a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473343,195,143 - 43,196,568 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473343,195,131 - 43,196,655 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scgb3a1
4 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:34
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000051916
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
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum total immunoglobulin E level (CMO:0001542)102291826836400810Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2298480Eau7Experimental allergic uveoretinitis QTL 70.0049uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)102795762634490668Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat

Markers in Region
RH139977  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21033,968,918 - 33,969,468 (+)MAPPERmRatBN7.2
Rnor_6.01035,134,421 - 35,134,970NCBIRnor6.0
Rnor_5.01034,905,940 - 34,906,489UniSTSRnor5.0
RGSC_v3.41035,126,429 - 35,126,978UniSTSRGSC3.4
Celera1033,325,440 - 33,325,989UniSTS
RH 3.4 Map10366.4UniSTS
Cytogenetic Map10q22UniSTS


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 renal system reproductive system respiratory system appendage
High
Medium 4 10
Low 1 3 16 2 19 2 1 2 8 2 12 1 1
Below cutoff 2 16 11 9 9 7 8 3 7 7 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000051916   ⟹   ENSRNOP00000045446
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1033,968,059 - 33,969,366 (+)Ensembl
Rnor_6.0 Ensembl1035,133,252 - 35,135,466 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113012   ⟹   ENSRNOP00000089765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1033,968,482 - 33,969,476 (+)Ensembl
RefSeq Acc Id: NM_001013180   ⟹   NP_001013198
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21033,968,059 - 33,969,366 (+)NCBI
Rnor_6.01035,133,561 - 35,134,868 (+)NCBI
Rnor_5.01034,905,080 - 34,906,387 (+)NCBI
RGSC_v3.41035,125,569 - 35,126,876 (+)RGD
Celera1033,324,580 - 33,325,887 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001013198 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAQ04483 (Get FASTA)   NCBI Sequence Viewer  
  DAA00359 (Get FASTA)   NCBI Sequence Viewer  
  EDM04227 (Get FASTA)   NCBI Sequence Viewer  
  EDM04228 (Get FASTA)   NCBI Sequence Viewer  
  EDM04229 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001013198   ⟸   NM_001013180
- Peptide Label: precursor
- UniProtKB: Q71MT8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000045446   ⟸   ENSRNOT00000051916
RefSeq Acc Id: ENSRNOP00000089765   ⟸   ENSRNOT00000113012

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9PU36-F1-model_v2 AlphaFold E9PU36 1-104 view protein structure

Transcriptome

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

Promoters
RGD ID:13697144
Promoter ID:EPDNEW_R7669
Type:single initiation site
Name:Scgb3a1_1
Description:secretoglobin, family 3A, member 1
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_6.01035,133,527 - 35,133,587EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727901 AgrOrtholog
BioCyc Gene G2FUF-25280 BioCyc
Ensembl Genes ENSRNOG00000002718 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045446 ENTREZGENE
  ENSRNOP00000045446.2 UniProtKB/TrEMBL
  ENSRNOP00000089765.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051916 ENTREZGENE
  ENSRNOT00000051916.4 UniProtKB/TrEMBL
  ENSRNOT00000113012.1 UniProtKB/TrEMBL
InterPro Secretoglobin_3A UniProtKB/TrEMBL
KEGG Report rno:338418 UniProtKB/TrEMBL
NCBI Gene 338418 ENTREZGENE
PANTHER PTHR34829 UniProtKB/TrEMBL
PhenoGen Scgb3a1 PhenoGen
UniProt A0A8I6AB14_RAT UniProtKB/TrEMBL
  E9PU36_RAT UniProtKB/TrEMBL
  Q71MT8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-11 Scgb3a1  secretoglobin, family 3A, member 1  Hin1  secretoglobin  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED