Hacd1 (3-hydroxyacyl-CoA dehydratase 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Hacd1 (3-hydroxyacyl-CoA dehydratase 1) Rattus norvegicus
Analyze
Symbol: Hacd1
Name: 3-hydroxyacyl-CoA dehydratase 1
RGD ID: 1595507
Description: Predicted to enable enzyme binding activity; hydro-lyase activity; and hydroxyapatite binding activity. Predicted to be involved in several processes, including cementum mineralization; fatty acid biosynthetic process; and positive regulation of cell-substrate adhesion. Predicted to act upstream of or within myotube differentiation; regulation of G1/S transition of mitotic cell cycle; and regulation of G2/M transition of mitotic cell cycle. Predicted to be located in endoplasmic reticulum. Predicted to be integral component of endoplasmic reticulum membrane. Orthologous to human HACD1 (3-hydroxyacyl-CoA dehydratase 1); PARTICIPATES IN unsaturated fatty acid biosynthetic pathway; INTERACTS WITH aconitine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC680115; protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a; protein tyrosine phosphatase-like protein A; protein-tyrosine phosphatase-like member A; Ptpla; similar to protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a isoform 1; very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21777,081,508 - 77,106,114 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1781,173,713 - 81,187,739 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01781,173,238 - 81,196,012 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01782,917,839 - 82,940,613 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41788,239,568 - 88,253,571 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1776,417,114 - 76,430,942 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:18554506   PMID:22067203   PMID:22106411   PMID:25263524  


Genomics

Comparative Map Data
Hacd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21777,081,508 - 77,106,114 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1781,173,713 - 81,187,739 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01781,173,238 - 81,196,012 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01782,917,839 - 82,940,613 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41788,239,568 - 88,253,571 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1776,417,114 - 76,430,942 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
HACD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1017,589,032 - 17,617,374 (-)EnsemblGRCh38hg38GRCh38
GRCh381017,589,032 - 17,617,374 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371017,631,031 - 17,659,373 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361017,671,964 - 17,699,379 (-)NCBINCBI36hg18NCBI36
Build 341017,672,275 - 17,699,379NCBI
Celera1017,565,146 - 17,593,075 (-)NCBI
Cytogenetic Map10p12.33NCBI
HuRef1017,544,972 - 17,572,460 (-)NCBIHuRef
CHM1_11017,632,313 - 17,659,761 (-)NCBICHM1_1
Hacd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39214,031,642 - 14,060,846 (-)NCBIGRCm39mm39
GRCm39 Ensembl213,855,093 - 14,060,946 (-)Ensembl
GRCm38214,026,831 - 14,056,035 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl213,850,282 - 14,056,135 (-)EnsemblGRCm38mm10GRCm38
MGSCv37213,948,458 - 13,977,662 (-)NCBIGRCm37mm9NCBIm37
MGSCv36213,944,585 - 13,973,789 (-)NCBImm8
Celera213,931,573 - 13,960,708 (-)NCBICelera
Cytogenetic Map2A1- A2NCBI
Hacd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542910,384,708 - 10,406,945 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542910,394,046 - 10,406,945 (+)NCBIChiLan1.0ChiLan1.0
HACD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11018,182,727 - 18,196,854 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1018,183,125 - 18,209,361 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01017,911,158 - 17,940,075 (-)NCBIMhudiblu_PPA_v0panPan3
HACD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1219,362,488 - 19,383,090 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl219,362,403 - 19,383,090 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,464,086 - 16,484,685 (+)NCBI
ROS_Cfam_1.0219,652,419 - 19,672,996 (+)NCBI
UMICH_Zoey_3.1216,855,006 - 16,875,380 (+)NCBI
UNSW_CanFamBas_1.0217,690,591 - 17,711,318 (+)NCBI
UU_Cfam_GSD_1.0218,310,361 - 18,330,963 (+)NCBI
Hacd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934418,233,190 - 18,244,697 (-)NCBI
SpeTri2.0NW_0049365209,716,178 - 9,725,949 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HACD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1043,897,161 - 43,929,409 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11043,901,590 - 43,929,441 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21048,592,803 - 48,619,692 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HACD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1917,537,945 - 17,565,831 (-)NCBI
Vero_WHO_p1.0NW_02366605123,182,977 - 23,210,775 (-)NCBI
Hacd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479610,295,957 - 10,315,222 (+)NCBI

Position Markers
RH141259  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21777,095,553 - 77,095,750 (+)MAPPERmRatBN7.2
Rnor_6.01781,185,520 - 81,185,716NCBIRnor6.0
Rnor_5.01782,930,121 - 82,930,317UniSTSRnor5.0
RGSC_v3.41788,251,380 - 88,251,576UniSTSRGSC3.4
Celera1776,428,751 - 76,428,947UniSTS
RH 3.4 Map17786.9UniSTS
Cytogenetic Map17q12.3UniSTS
BE099735  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map17786.9UniSTS
Cytogenetic Map17q12.3UniSTS
AA893268  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21777,091,163 - 77,091,413 (+)MAPPERmRatBN7.2
Rnor_6.01781,181,130 - 81,181,379NCBIRnor6.0
Rnor_5.01782,925,731 - 82,925,980UniSTSRnor5.0
RGSC_v3.41788,246,990 - 88,247,239UniSTSRGSC3.4
Celera1776,424,381 - 76,424,630UniSTS
Cytogenetic Map17q12.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175622429686731080Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)176219582286194199Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176549735982019219Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176751265790843779Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176933327285183543Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177485263085183543Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177570542786731080Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:88
Count of miRNA genes:83
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000063911
Prediction methods:Microtar, 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.


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 2 43 22 14 5 14 8 11 36 22 32 10 8
Low 1 35 27 14 27 38 13 9 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000063911   ⟹   ENSRNOP00000059743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1781,173,713 - 81,187,739 (-)Ensembl
RefSeq Acc Id: NM_001101001   ⟹   NP_001094471
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,083,742 - 77,106,048 (-)NCBI
Rnor_6.01781,173,708 - 81,196,012 (-)NCBI
Rnor_5.01782,917,839 - 82,940,613 (-)NCBI
RGSC_v3.41788,239,568 - 88,253,571 (-)RGD
Celera1776,417,114 - 76,430,942 (-)RGD
Sequence:
RefSeq Acc Id: XM_039096059   ⟹   XP_038951987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,081,510 - 77,106,113 (-)NCBI
RefSeq Acc Id: XM_039096060   ⟹   XP_038951988
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,085,516 - 77,106,114 (-)NCBI
RefSeq Acc Id: XM_039096061   ⟹   XP_038951989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,094,080 - 77,106,114 (-)NCBI
RefSeq Acc Id: XR_005495327
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,081,508 - 77,106,114 (-)NCBI
RefSeq Acc Id: XR_005495328
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,081,508 - 77,106,112 (-)NCBI
RefSeq Acc Id: XR_005495329
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,085,516 - 77,106,114 (-)NCBI
RefSeq Acc Id: XR_005495330
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,085,534 - 77,106,114 (-)NCBI
RefSeq Acc Id: XR_005495331
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21777,081,508 - 77,106,113 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001094471   ⟸   NM_001101001
- UniProtKB: A1IVX5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059743   ⟸   ENSRNOT00000063911
RefSeq Acc Id: XP_038951987   ⟸   XM_039096059
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951988   ⟸   XM_039096060
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951989   ⟸   XM_039096061
- Peptide Label: isoform X3

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595507 AgrOrtholog
Ensembl Genes ENSRNOG00000043192 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059743 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000063911 UniProtKB/TrEMBL
InterPro Tyr_Pase-like_PTPLA UniProtKB/TrEMBL
KEGG Report rno:680115 UniProtKB/TrEMBL
NCBI Gene 680115 ENTREZGENE
PANTHER PTPLA UniProtKB/TrEMBL
Pfam PTPLA UniProtKB/TrEMBL
PhenoGen Hacd1 PhenoGen
UniProt A1IVX5 ENTREZGENE, UniProtKB/TrEMBL
  F1LSK3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-02-04 Hacd1  3-hydroxyacyl-CoA dehydratase 1  Ptpla  protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Ptpla  protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a  LOC683916  similar to protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a isoform 1  Data Merged 1643240 APPROVED
2008-03-05 Ptpla  protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a  LOC680115  similar to protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC680115  similar to protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC683916  similar to protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL