Tafa2 (TAFA chemokine like family member 2) - Rat Genome Database
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Gene: Tafa2 (TAFA chemokine like family member 2) Rattus norvegicus
Analyze
Symbol: Tafa2
Name: TAFA chemokine like family member 2
RGD ID: 1589429
Description: Predicted to have receptor ligand activity. Predicted to be involved in memory and visual learning. Predicted to localize to cytoplasm; extracellular space; and nucleus. Orthologous to human TAFA2 (TAFA chemokine like family member 2); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: chemokine-like protein TAFA-2; Fam19a2; family with sequence similarity 19 (chemokine (C-C motif)-like), member A2; family with sequence similarity 19 member A2, C-C motif chemokine like; hypothetical protein LOC678999; LOC680647; similar to TAFA2 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Fam19a2Tn(sb-T2/Bart3)2.184Mcwi  
Genetic Models: F344-Fam19a2Tn(sb-T2/Bart3)2.184Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2758,942,598 - 59,418,640 (+)NCBI
Rnor_6.0 Ensembl766,017,086 - 66,172,360 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0766,017,066 - 66,496,690 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0766,221,368 - 66,695,803 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4763,388,665 - 63,566,226 (+)NCBIRGSC3.4rn4RGSC3.4
Celera756,114,065 - 56,588,451 (+)NCBICelera
Cytogenetic Map7q22NCBI
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

Additional References at PubMed
PMID:30137205  


Genomics

Comparative Map Data
Tafa2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2758,942,598 - 59,418,640 (+)NCBI
Rnor_6.0 Ensembl766,017,086 - 66,172,360 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0766,017,066 - 66,496,690 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0766,221,368 - 66,695,803 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4763,388,665 - 63,566,226 (+)NCBIRGSC3.4rn4RGSC3.4
Celera756,114,065 - 56,588,451 (+)NCBICelera
Cytogenetic Map7q22NCBI
TAFA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1261,708,259 - 62,279,150 (-)EnsemblGRCh38hg38GRCh38
GRCh381261,708,273 - 62,260,104 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371262,102,054 - 62,586,554 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh371262,102,029 - 62,586,620 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361260,388,307 - 60,872,818 (-)NCBINCBI36hg18NCBI36
Build 341260,388,309 - 60,872,818NCBI
Celera1261,771,461 - 62,255,544 (-)NCBI
Cytogenetic Map12q14.1NCBI
HuRef1259,153,030 - 59,637,513 (-)NCBIHuRef
CHM1_11262,069,825 - 62,554,522 (-)NCBICHM1_1
Tafa2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910123,099,813 - 123,577,109 (+)NCBIGRCm39mm39
GRCm3810123,264,024 - 123,741,204 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10123,263,996 - 123,741,204 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710122,701,132 - 123,178,035 (+)NCBIGRCm37mm9NCBIm37
MGSCv3610122,667,136 - 123,144,039 (+)NCBImm8
Celera10125,646,982 - 126,120,933 (+)NCBICelera
Cytogenetic Map10D2NCBI
Tafa2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554588,935,792 - 9,351,358 (-)NCBIChiLan1.0ChiLan1.0
TAFA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11226,954,142 - 27,501,208 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1227,225,154 - 27,502,300 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01226,683,045 - 27,229,772 (+)NCBIMhudiblu_PPA_v0panPan3
TAFA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl104,999,695 - 5,233,553 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1104,998,538 - 5,134,970 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tafa2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936545517,910 - 936,630 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAFA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl526,391,992 - 26,559,821 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1526,391,969 - 26,893,517 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2528,995,477 - 29,036,460 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TAFA2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11157,598,179 - 58,095,527 (-)NCBI
ChlSab1.1 Ensembl1157,597,697 - 57,763,149 (-)Ensembl
Tafa2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248025,682,672 - 6,275,081 (+)NCBI

Position Markers
D7Rat166  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0766,210,469 - 66,210,636NCBIRnor6.0
Rnor_5.0766,411,716 - 66,411,883UniSTSRnor5.0
RGSC_v3.4763,349,606 - 63,349,774RGDRGSC3.4
RGSC_v3.4763,349,607 - 63,349,774UniSTSRGSC3.4
RGSC_v3.1763,370,210 - 63,370,585RGD
Celera756,396,145 - 56,396,312UniSTS
FHH x ACI Map733.38RGD
FHH x ACI Map733.38UniSTS
Cytogenetic Map7q22UniSTS
D7Rat57  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0766,237,933 - 66,238,149NCBIRnor6.0
Rnor_5.0766,438,174 - 66,438,390UniSTSRnor5.0
RGSC_v3.4763,324,498 - 63,324,715RGDRGSC3.4
RGSC_v3.4763,324,499 - 63,324,715UniSTSRGSC3.4
RGSC_v3.1763,345,228 - 63,345,445RGD
Celera756,371,462 - 56,371,674UniSTS
FHH x ACI Map733.38RGD
FHH x ACI Map733.38UniSTS
Cytogenetic Map7q22UniSTS
D4Mit353  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01426,098,556 - 26,098,623NCBIRnor6.0
Rnor_6.0766,437,812 - 66,437,879NCBIRnor6.0
Rnor_5.01425,927,493 - 25,927,560UniSTSRnor5.0
Rnor_5.0766,636,936 - 66,637,003UniSTSRnor5.0
RGSC_v3.4763,119,310 - 63,119,377UniSTSRGSC3.4
RGSC_v3.41426,040,509 - 26,040,576UniSTSRGSC3.4
Celera756,172,983 - 56,173,050UniSTS
Celera1423,565,134 - 23,565,201UniSTS
Celera679,726,093 - 79,726,163UniSTS
Cytogenetic Map7q22UniSTS
AI501937  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0766,017,236 - 66,017,450NCBIRnor6.0
Rnor_5.0766,221,525 - 66,221,739UniSTSRnor5.0
RGSC_v3.4763,552,887 - 63,553,101UniSTSRGSC3.4
Celera756,588,067 - 56,588,281UniSTS
Cytogenetic Map7q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)72216841267168412Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)72473146569731465Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72820465373204653Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)73138152976381529Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)73203505377035053Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)73257294277572942Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)73304444971352127Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)73586772980867729Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)73586772993155402Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73854770683547706Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)74087268285872682Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)74087268285872682Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74530157390301573Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)75025210395252103Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)75079381895793818Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)751252005111589099Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)75320034498200344Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)75425951299259512Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)75453499673293934Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)75507286269399731Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)755495689100495689Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)755495689100495689Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)755495689100495689Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)755495689100495689Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)755495689100495689Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)755495689100495689Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)755495689100495689Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)761047589113228378Rat


Genetic Models
This gene Tafa2 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:102
Interacting mature miRNAs:111
Transcripts:ENSRNOT00000005537
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 4 56
Low 3 21 12 12 1 12 16 18 34 2
Below cutoff 18 31 25 7 25 8 9 2 17 7 8 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005537   ⟹   ENSRNOP00000005537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl766,017,086 - 66,172,360 (-)Ensembl
RefSeq Acc Id: XM_008765430   ⟹   XP_008763652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0766,017,066 - 66,496,689 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008776449   ⟹   XP_008774671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera756,114,065 - 56,588,451 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595215   ⟹   XP_017450704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2759,151,840 - 59,418,640 (+)NCBI
Rnor_6.0766,017,066 - 66,496,690 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595216   ⟹   XP_017450705
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0766,017,066 - 66,393,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595217   ⟹   XP_017450706
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0766,017,066 - 66,435,976 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017603429   ⟹   XP_017458918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera756,114,065 - 56,588,451 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603430   ⟹   XP_017458919
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera756,323,378 - 56,588,451 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603431   ⟹   XP_017458920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera756,214,011 - 56,588,451 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603432   ⟹   XP_017458921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera756,175,174 - 56,588,451 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039080145   ⟹   XP_038936073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2759,151,838 - 59,418,640 (+)NCBI
RefSeq Acc Id: XM_039080146   ⟹   XP_038936074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2759,040,366 - 59,418,640 (+)NCBI
RefSeq Acc Id: XM_039080147   ⟹   XP_038936075
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2759,002,857 - 59,418,640 (+)NCBI
RefSeq Acc Id: XM_039080148   ⟹   XP_038936076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2758,942,598 - 59,418,640 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_008774671   ⟸   XM_008776449
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008763652   ⟸   XM_008765430
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017458918   ⟸   XM_017603429
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017458921   ⟸   XM_017603432
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017458920   ⟸   XM_017603431
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017458919   ⟸   XM_017603430
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017450704   ⟸   XM_017595215
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450706   ⟸   XM_017595217
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017450705   ⟸   XM_017595216
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000005537   ⟸   ENSRNOT00000005537
RefSeq Acc Id: XP_038936076   ⟸   XM_039080148
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038936075   ⟸   XM_039080147
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038936074   ⟸   XM_039080146
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038936073   ⟸   XM_039080145
- Peptide Label: isoform X1

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)
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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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/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
LL/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
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:1589429 AgrOrtholog
Ensembl Genes ENSRNOG00000004180 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005537 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005537 UniProtKB/TrEMBL
InterPro Chemokine-like_FAM19A2 UniProtKB/TrEMBL
NCBI Gene 680647 ENTREZGENE
Pfam TAFA UniProtKB/TrEMBL
PhenoGen Tafa2 PhenoGen
Transposagen LOC680647 Transposagen
UniProt F1LV54_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Fam19a2  family with sequence similarity 19 (chemokine (C-C motif)-like), member A2  LOC678999  hypothetical protein LOC678999  Data Merged 1643240 APPROVED
2008-03-05 Fam19a2  family with sequence similarity 19 (chemokine (C-C motif)-like), member A2  LOC680647  similar to TAFA2 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC678999  hypothetical protein LOC678999      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC680647  similar to TAFA2 protein      Symbol and Name status set to provisional 70820 PROVISIONAL