Degs2 (delta(4)-desaturase, sphingolipid 2) - Rat Genome Database

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Gene: Degs2 (delta(4)-desaturase, sphingolipid 2) Rattus norvegicus
Analyze
Symbol: Degs2
Name: delta(4)-desaturase, sphingolipid 2
RGD ID: 1305023
Description: Predicted to have sphingolipid delta-4 desaturase activity and sphingosine hydroxylase activity. Predicted to be involved in ceramide biosynthetic process and sphinganine metabolic process. Predicted to localize to endoplasmic reticulum membrane and integral component of membrane. Orthologous to human DEGS2 (delta 4-desaturase, sphingolipid 2); PARTICIPATES IN Fabry disease pathway; Gaucher's disease pathway; Krabbe disease pathway; INTERACTS WITH 17beta-estradiol 3-benzoate; 6-propyl-2-thiouracil; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: degenerative spermatocyte homolog 2 (Drosophila), lipid desaturase; degenerative spermatocyte homolog 2, lipid desaturase (Drosophila); LOC314438; MGC112667; RGD1305023; similar to RIKEN cDNA 2210008A03 gene; sphingolipid 4-desaturase; sphingolipid C4-hydroxylase/delta 4-desaturase; sphingolipid C4-monooxygenase; sphingolipid delta(4)-desaturase/C4-hydroxylase DES2; sphingolipid delta(4)-desaturase/C4-monooxygenase DES2
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
mRatBN7.26127,596,063 - 127,613,293 (-)NCBI
Rnor_6.0 Ensembl6132,591,969 - 132,608,600 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06132,591,968 - 132,608,600 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06141,762,044 - 141,778,676 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46133,021,596 - 133,037,633 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16133,028,029 - 133,043,753 (-)NCBI
Celera6125,151,076 - 125,165,766 (-)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11937514   PMID:12477932   PMID:15474011   PMID:16571104   PMID:17716801   PMID:21914808  


Genomics

Comparative Map Data
Degs2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26127,596,063 - 127,613,293 (-)NCBI
Rnor_6.0 Ensembl6132,591,969 - 132,608,600 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06132,591,968 - 132,608,600 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06141,762,044 - 141,778,676 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46133,021,596 - 133,037,633 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16133,028,029 - 133,043,753 (-)NCBI
Celera6125,151,076 - 125,165,766 (-)NCBICelera
Cytogenetic Map6q32NCBI
DEGS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl14100,143,957 - 100,159,645 (-)EnsemblGRCh38hg38GRCh38
GRCh3814100,143,957 - 100,166,886 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714100,610,294 - 100,625,982 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361499,682,509 - 99,695,712 (-)NCBINCBI36hg18NCBI36
Build 341499,682,509 - 99,695,712NCBI
Celera1480,667,585 - 80,680,837 (-)NCBI
Cytogenetic Map14q32.2NCBI
HuRef1480,794,810 - 80,808,042 (-)NCBIHuRef
CHM1_114100,550,475 - 100,563,702 (-)NCBICHM1_1
Degs2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912108,653,051 - 108,668,561 (-)NCBIGRCm39mm39
GRCm39 Ensembl12108,644,970 - 108,668,570 (-)Ensembl
GRCm3812108,686,792 - 108,702,306 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12108,678,711 - 108,702,315 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712109,925,002 - 109,940,516 (-)NCBIGRCm37mm9NCBIm37
MGSCv3612109,138,034 - 109,150,097 (-)NCBImm8
Celera12109,922,978 - 109,938,475 (-)NCBICelera
Cytogenetic Map12F1NCBI
Degs2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543821,300,118 - 21,313,330 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543821,300,118 - 21,313,330 (-)NCBIChiLan1.0ChiLan1.0
DEGS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.114100,086,782 - 100,100,741 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl14100,086,782 - 100,100,741 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01480,767,334 - 80,813,506 (-)NCBIMhudiblu_PPA_v0panPan3
DEGS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1868,461,461 - 68,483,685 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl868,462,555 - 68,533,062 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha867,982,593 - 68,003,272 (-)NCBI
ROS_Cfam_1.0868,746,674 - 68,768,529 (-)NCBI
UMICH_Zoey_3.1868,408,727 - 68,430,548 (-)NCBI
UNSW_CanFamBas_1.0868,474,055 - 68,496,021 (-)NCBI
UU_Cfam_GSD_1.0868,871,727 - 68,893,581 (-)NCBI
Degs2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086406,211,662 - 6,260,794 (+)NCBI
SpeTri2.0NW_0049366043,821,672 - 3,839,975 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DEGS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7121,058,101 - 121,076,329 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17121,058,102 - 121,131,612 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27128,592,520 - 128,599,969 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DEGS2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12478,114,950 - 78,128,766 (-)NCBI
ChlSab1.1 Ensembl2478,115,292 - 78,127,831 (-)Ensembl
Vero_WHO_p1.0NW_02366605365,248,542 - 65,263,548 (-)NCBI
Degs2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247343,913,159 - 3,925,309 (+)NCBI

Position Markers
D6Got181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,601,113 - 127,601,226 (+)MAPPER
Rnor_6.06132,597,014 - 132,597,126NCBIRnor6.0
Rnor_5.06141,767,090 - 141,767,202UniSTSRnor5.0
RGSC_v3.46133,026,644 - 133,026,751RGDRGSC3.4
RGSC_v3.46133,026,644 - 133,026,756UniSTSRGSC3.4
RGSC_v3.16133,032,831 - 133,032,943RGD
Celera6125,156,123 - 125,156,235UniSTS
RH 3.4 Map6790.1UniSTS
RH 3.4 Map6790.1RGD
RH 2.0 Map61112.2RGD
Cytogenetic Map6q32UniSTS
RH132042  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,596,171 - 127,596,361 (+)MAPPER
Rnor_6.06132,592,072 - 132,592,261NCBIRnor6.0
Rnor_5.06141,762,148 - 141,762,337UniSTSRnor5.0
RGSC_v3.46133,021,700 - 133,021,889UniSTSRGSC3.4
Celera6125,151,180 - 125,151,369UniSTS
RH 3.4 Map6791.1UniSTS
Cytogenetic Map6q32UniSTS
AI852933  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,596,283 - 127,596,403 (+)MAPPER
Rnor_6.06132,592,184 - 132,592,303NCBIRnor6.0
Rnor_5.06141,762,260 - 141,762,379UniSTSRnor5.0
RGSC_v3.46133,021,812 - 133,021,931UniSTSRGSC3.4
Celera6125,151,292 - 125,151,411UniSTS
Cytogenetic Map6q32UniSTS
D6Got181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,601,114 - 127,601,221 (+)MAPPER
Rnor_6.06132,597,015 - 132,597,121NCBIRnor6.0
Rnor_5.06141,767,091 - 141,767,197UniSTSRnor5.0
RGSC_v3.46133,026,645 - 133,026,751UniSTSRGSC3.4
Celera6125,156,124 - 125,156,230UniSTS
Cytogenetic Map6q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6108154445133849286Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6117355600147991367Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6121224054135658578Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6127286494144745573Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6127286494147249902Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6127286494147991367Rat
2312560Pur20Proteinuria QTL 202.10.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6130561943144745573Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:141
Count of miRNA genes:113
Interacting mature miRNAs:120
Transcripts:ENSRNOT00000015855
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.


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 3 6 6 31 4
Low 28 25 13 25 37 4 27 11
Below cutoff 24 20 14 14 7 8 23 10 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015855   ⟹   ENSRNOP00000015855
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6132,591,969 - 132,608,600 (-)Ensembl
RefSeq Acc Id: NM_001017457   ⟹   NP_001017457
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26127,596,068 - 127,613,293 (-)NCBI
Rnor_6.06132,591,968 - 132,608,600 (-)NCBI
Rnor_5.06141,762,044 - 141,778,676 (-)NCBI
RGSC_v3.46133,021,596 - 133,037,633 (-)RGD
Celera6125,151,076 - 125,165,766 (-)RGD
Sequence:
RefSeq Acc Id: XM_039112401   ⟹   XP_038968329
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26127,596,063 - 127,609,222 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001017457 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968329 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98701 (Get FASTA)   NCBI Sequence Viewer  
  CAI79417 (Get FASTA)   NCBI Sequence Viewer  
  EDL97561 (Get FASTA)   NCBI Sequence Viewer  
  Q564G3 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001017457   ⟸   NM_001017457
- UniProtKB: Q564G3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000015855   ⟸   ENSRNOT00000015855
RefSeq Acc Id: XP_038968329   ⟸   XM_039112401
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13694820
Promoter ID:EPDNEW_R5344
Type:initiation region
Name:Degs2_1
Description:delta-desaturase, sphingolipid 2
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_6.06132,608,565 - 132,608,625EPDNEW

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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:1305023 AgrOrtholog
Ensembl Genes ENSRNOG00000011716 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000015855 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000015855 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7387212 IMAGE-MGC_LOAD
InterPro DES1/DES2 UniProtKB/Swiss-Prot
  FA_desaturase_dom UniProtKB/Swiss-Prot
  Sphingolipid_d4-desaturase_N UniProtKB/Swiss-Prot
KEGG Report rno:314438 UniProtKB/Swiss-Prot
MGC_CLONE MGC:112667 IMAGE-MGC_LOAD
NCBI Gene 314438 ENTREZGENE
Pfam FA_desaturase UniProtKB/Swiss-Prot
  Lipid_DES UniProtKB/Swiss-Prot
PhenoGen Degs2 PhenoGen
PIRSF Sphnglp_dlt4_des UniProtKB/Swiss-Prot
SMART Lipid_DES UniProtKB/Swiss-Prot
UniProt DEGS2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-07-16 Degs2  delta(4)-desaturase, sphingolipid 2  Degs2  degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Degs2  degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)  Degs2  degenerative spermatocyte homolog 2 (Drosophila), lipid desaturase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Degs2  degenerative spermatocyte homolog 2 (Drosophila), lipid desaturase  RGD1305023  similar to RIKEN cDNA 2210008A03 gene  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1305023  similar to RIKEN cDNA 2210008A03 gene  RGD1305023_predicted  similar to RIKEN cDNA 2210008A03 gene (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1305023_predicted  similar to RIKEN cDNA 2210008A03 gene (predicted)  LOC314438_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC314438_predicted  similar to RIKEN cDNA 2210008A03 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL