C4a (complement C4A) - Rat Genome Database

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Gene: C4a (complement C4A) Rattus norvegicus
Analyze
Symbol: C4a
Name: complement C4A
RGD ID: 620005
Description: Predicted to have complement component C1q complex binding activity. Predicted to be involved in complement activation and positive regulation of apoptotic cell clearance. Localizes to extracellular space. Human ortholog(s) of this gene implicated in autistic disorder; autoimmune disease (multiple); complement deficiency (multiple); and renal cell carcinoma. Orthologous to several human genes including C4B (complement C4B (Chido blood group)); PARTICIPATES IN classical complement pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: C4; C4-1; C4b; complement C4; complement C4-like; complement component 4 (within H-2S); complement component 4, gene 1; complement component 4a; complement component 4A (Rodgers blood group); complement component 4B (Chido blood group); complement component 4B (Childo blood group); LOC102549354; LOC103689965
RGD Orthologs
Human
Mouse
Squirrel
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,005,731 - 4,020,083 (+)NCBI
Rnor_6.0 Ensembl202,651,599 - 2,678,141 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0202,651,599 - 2,678,183 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,573,225 - 6,587,996 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0204,754,468 - 4,755,821 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,106,123 - 4,145,904NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1204,106,391 - 4,316,103NCBI
Celera204,010,655 - 4,024,973 (-)NCBICelera
Cytogenetic Map20p12NCBI
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

Cellular Component
axon  (IEA,ISO)
dendrite  (IEA,ISO)
extracellular region  (IDA,IEA)
extracellular space  (IBA,IDA,IEA,ISO)
neuronal cell body  (ISO)
synapse  (IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1438267   PMID:2395880   PMID:3023818   PMID:3262196   PMID:8133084   PMID:12136338   PMID:15060079   PMID:17204478   PMID:17345707   PMID:19302245   PMID:23613499   PMID:25645918  
PMID:26219954   PMID:26316108   PMID:26814963  


Genomics

Comparative Map Data
C4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,005,731 - 4,020,083 (+)NCBI
Rnor_6.0 Ensembl202,651,599 - 2,678,141 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0202,651,599 - 2,678,183 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,573,225 - 6,587,996 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0204,754,468 - 4,755,821 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,106,123 - 4,145,904NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1204,106,391 - 4,316,103NCBI
Celera204,010,655 - 4,024,973 (-)NCBICelera
Cytogenetic Map20p12NCBI
C4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl631,982,057 - 32,002,681 (+)EnsemblGRCh38hg38GRCh38
GRCh38631,982,057 - 32,002,681 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37631,949,834 - 31,970,458 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,090,549 - 32,111,173 (+)NCBINCBI36hg18NCBI36
Build 34632,090,549 - 32,111,173NCBI
Celera633,549,596 - 33,570,218 (+)NCBI
Cytogenetic Map6p21.33NCBI
HuRef631,736,844 - 31,746,589 (+)NCBIHuRef
CHM1_1631,951,915 - 31,972,655 (+)NCBICHM1_1
C4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,028,069 - 35,042,436 (-)NCBIGRCm39mm39
GRCm39 Ensembl1735,028,069 - 35,042,440 (-)Ensembl
GRCm381734,809,092 - 34,823,460 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,809,092 - 34,823,464 (-)EnsemblGRCm38mm10GRCm38
MGSCv371734,946,037 - 34,960,399 (-)NCBIGRCm37mm9NCBIm37
MGSCv361734,417,150 - 34,431,510 (-)NCBImm8
Celera1737,904,407 - 37,918,769 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.37NCBI
LOC101975827
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,991,270 - 36,005,133 (+)NCBI
SpeTri2.0NW_0049367271,556,204 - 1,570,084 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0

Position Markers
D20Yum59  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,031,068 - 4,031,242 (-)MAPPER
Rnor_6.0204,481,956 - 4,482,129NCBIRnor6.0
Rnor_5.0206,561,312 - 6,561,485UniSTSRnor5.0
RGSC_v3.4204,132,407 - 4,132,580UniSTSRGSC3.4
Celera203,998,885 - 3,999,058UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:76
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000072377
Prediction methods:Microtar, 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.


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 nervous system renal system reproductive system respiratory system
High
Medium
Low
Below cutoff 1 1 34 22 16 22 3 1 10 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000514   ⟹   ENSRNOP00000000514
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,495,465 - 4,508,214 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000072377   ⟹   ENSRNOP00000066721
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl202,651,702 - 2,678,141 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078871   ⟹   ENSRNOP00000068572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl202,651,599 - 2,652,952 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083833   ⟹   ENSRNOP00000069352
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl202,667,524 - 2,678,141 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086027   ⟹   ENSRNOP00000069699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,302,347 - 4,508,197 (-)Ensembl
RefSeq Acc Id: NM_031504   ⟹   NP_113692
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,005,731 - 4,020,083 (+)NCBI
Rnor_6.0202,651,599 - 2,678,183 (-)NCBI
Rnor_5.0204,754,468 - 4,755,821 (-)NCBI
Rnor_5.0206,573,225 - 6,587,996 (-)NCBI
RGSC_v3.4204,106,123 - 4,145,904 (+)RGD
Celera204,010,655 - 4,024,973 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_113692 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAM14719 (Get FASTA)   NCBI Sequence Viewer  
  AAN72415 (Get FASTA)   NCBI Sequence Viewer  
  CAE83967 (Get FASTA)   NCBI Sequence Viewer  
  P08649 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_113692   ⟸   NM_031504
- Peptide Label: precursor
- UniProtKB: P08649 (UniProtKB/Swiss-Prot),   Q6MG79 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069352   ⟸   ENSRNOT00000083833
RefSeq Acc Id: ENSRNOP00000066721   ⟸   ENSRNOT00000072377
RefSeq Acc Id: ENSRNOP00000068572   ⟸   ENSRNOT00000078871
RefSeq Acc Id: ENSRNOP00000069699   ⟸   ENSRNOT00000086027
RefSeq Acc Id: ENSRNOP00000000514   ⟸   ENSRNOT00000000514
Protein Domains
Anaphylatoxin-like   NTR

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)
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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:620005 AgrOrtholog
  RGD:9245878 AgrOrtholog
Ensembl Genes ENSRNOG00000000443 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000047657 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000514 UniProtKB/TrEMBL
  ENSRNOP00000066721 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068572 UniProtKB/TrEMBL
  ENSRNOP00000069352 UniProtKB/TrEMBL
  ENSRNOP00000069699 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000514 UniProtKB/TrEMBL
  ENSRNOT00000072377 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078871 UniProtKB/TrEMBL
  ENSRNOT00000083833 UniProtKB/TrEMBL
  ENSRNOT00000086027 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.120 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.690 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro A-macroglobulin_rcpt-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  A-macroglobulin_rcpt-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  A2M_N_BRD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Alpha-macroglobulin_TED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Anaphylatoxin/fibulin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Anaphylatoxin_comp_syst UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Anaphylatoxn_comp_syst_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Complement_C4A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Macroglobln_a2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MacrogloblnA2_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MG2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MG3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MG4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Netrin_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Netrin_module_non-TIMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Terpenoid_cyclase/PrenylTrfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIMP-like_OB-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:103689965 UniProtKB/TrEMBL
  rno:24233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 24233 ENTREZGENE
PANTHER PTHR11412:SF86 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam A2M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  A2M_BRD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  A2M_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ANATO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MG2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MG3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MG4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TED_complement UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen C4a PhenoGen
PRINTS ANAPHYLATOXN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ALPHA_2_MACROGLOBULIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ANAPHYLATOXIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ANAPHYLATOXIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART A2M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  A2M_N_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  A2M_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ANATO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C345C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47686 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48239 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49410 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50242 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JT52_RAT UniProtKB/TrEMBL
  A0A0G2JV52_RAT UniProtKB/TrEMBL
  A0A0G2JW12_RAT UniProtKB/TrEMBL
  CO4_RAT UniProtKB/Swiss-Prot
  F1LNM4_RAT UniProtKB/TrEMBL
  M0RB00_RAT UniProtKB/TrEMBL
  P08649 ENTREZGENE
  Q6MG79 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q62895 UniProtKB/Swiss-Prot
  Q8R403 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 C4a  complement C4A  LOC103689965  complement C4-like  Data Merged 737654 PROVISIONAL
2018-05-07 C4a  complement C4A  C4a  complement component 4A (Rodgers blood group)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 C4a  complement component 4A (Rodgers blood group)  LOC102549354  complement C4-like  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103689965  complement C4-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-12-18 LOC102549354  complement C4-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-02-22 C4a  complement component 4A (Rodgers blood group)  C4b  complement component 4B (Chido blood group)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 C4b  complement component 4B (Chido blood group)  C4b  complement component 4B (Childo blood group)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 C4b  complement component 4B (Childo blood group)  C4a  complement component 4a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 C4a  complement component 4a      Symbol and Name updated 629477 APPROVED
2003-03-10 C4a  complement component 4a  C4  Complement component 4  Data Merged 628472 PROVISIONAL
2002-08-07 C4a        Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 C4  Complement component 4      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_mapping maps to the MHC RT1 complex 1300431