Shld2 (shieldin complex subunit 2) - Rat Genome Database
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Gene: Shld2 (shieldin complex subunit 2) Rattus norvegicus
Analyze
Symbol: Shld2
Name: shieldin complex subunit 2
RGD ID: 1565067
Description: Predicted to be involved in negative regulation of double-strand break repair via homologous recombination; positive regulation of double-strand break repair via nonhomologous end joining; and positive regulation of isotype switching. Predicted to localize to nucleus and site of double-strand break. Orthologous to human SHLD2 (shieldin complex subunit 2); INTERACTS WITH bisphenol A; dieldrin; (-)-epigallocatechin 3-gallate (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Fam35a; family with sequence similarity 35, member A; hypothetical protein LOC364514; LOC364514; RGD1310009; uncharacterized protein LOC364514
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
Rnor_6.01610,570,307 - 10,661,528 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,570,314 - 10,661,528 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0168,888,929 - 8,979,969 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4169,868,212 - 9,965,225 (-)NCBIRGSC3.4rn4RGSC3.4
Celera165,576,833 - 5,667,636 (+)NCBICelera
Cytogenetic Map16p15NCBI
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

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:29656893   PMID:29789392  


Genomics

Comparative Map Data
Shld2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01610,570,307 - 10,661,528 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,570,314 - 10,661,528 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0168,888,929 - 8,979,969 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4169,868,212 - 9,965,225 (-)NCBIRGSC3.4rn4RGSC3.4
Celera165,576,833 - 5,667,636 (+)NCBICelera
Cytogenetic Map16p15NCBI
SHLD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1087,094,161 - 87,191,468 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1087,094,161 - 87,191,465 (+)EnsemblGRCh38hg38GRCh38
GRCh381087,094,478 - 87,191,468 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371088,854,953 - 88,951,225 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361088,844,933 - 88,941,202 (+)NCBINCBI36hg18NCBI36
Build 341088,844,932 - 88,941,200NCBI
Cytogenetic Map10q23.2NCBI
HuRef1082,778,394 - 82,789,042 (+)NCBIHuRef
CHM1_11089,136,724 - 89,232,977 (+)NCBICHM1_1
Shld2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391433,958,905 - 34,032,528 (-)NCBIGRCm39mm39
GRCm381434,236,948 - 34,310,651 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1434,237,033 - 34,310,493 (-)EnsemblGRCm38mm10GRCm38
MGSCv371435,050,219 - 35,123,689 (-)NCBIGRCm37mm9NCBIm37
MGSCv361433,066,133 - 33,139,458 (-)NCBImm8
Celera1430,499,098 - 30,576,001 (-)NCBICelera
Cytogenetic Map14BNCBI
Shld2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555106,075,510 - 6,114,898 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555106,021,477 - 6,114,745 (+)NCBIChiLan1.0ChiLan1.0
LOC103784056
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11487,923,049 - 87,928,101 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01043,572,547 - 43,624,201 (+)NCBIMhudiblu_PPA_v0panPan3
SHLD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl434,688,245 - 34,763,705 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1434,665,111 - 34,740,645 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Shld2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366015,315,297 - 5,400,752 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHLD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1488,005,590 - 88,121,383 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11488,005,599 - 88,121,155 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21495,538,054 - 95,600,923 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SHLD2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1944,565,105 - 44,652,926 (-)NCBI
ChlSab1.1 Ensembl944,564,792 - 44,605,562 (-)Ensembl
Shld2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462484121,077 - 133,155 (-)NCBI

Position Markers
D16Mgh3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01610,660,513 - 10,660,736NCBIRnor6.0
Rnor_5.0168,978,954 - 8,979,177UniSTSRnor5.0
RGSC_v3.4169,964,209 - 9,964,433RGDRGSC3.4
RGSC_v3.4169,964,210 - 9,964,433UniSTSRGSC3.4
RGSC_v3.1169,964,207 - 9,964,431RGD
Celera165,577,625 - 5,577,848UniSTS
Cytogenetic Map16p16UniSTS
D16Rat111  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01610,632,323 - 10,632,475NCBIRnor6.0
Rnor_5.0168,950,916 - 8,951,068UniSTSRnor5.0
RGSC_v3.4169,936,041 - 9,936,194RGDRGSC3.4
RGSC_v3.4169,936,042 - 9,936,194UniSTSRGSC3.4
RGSC_v3.1169,935,977 - 9,936,344RGD
Celera165,605,767 - 5,605,907UniSTS
Cytogenetic Map16p16UniSTS
FHH x ACI Map165.4199UniSTS
FHH x ACI Map165.4199RGD
D16Mco9  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01610,660,521 - 10,660,724NCBIRnor6.0
Rnor_5.0168,978,962 - 8,979,165UniSTSRnor5.0
RGSC_v3.4169,964,217 - 9,964,421RGDRGSC3.4
RGSC_v3.4169,964,218 - 9,964,421UniSTSRGSC3.4
RGSC_v3.1169,964,215 - 9,964,419RGD
Celera165,577,637 - 5,577,840UniSTS
Cytogenetic Map16p16UniSTS
D16Arb11  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01610,660,789 - 10,660,990NCBIRnor6.0
Rnor_5.0168,979,230 - 8,979,431UniSTSRnor5.0
RGSC_v3.4169,964,485 - 9,964,687RGDRGSC3.4
RGSC_v3.4169,964,486 - 9,964,687UniSTSRGSC3.4
RGSC_v3.1169,964,483 - 9,964,685RGD
Celera165,577,371 - 5,577,572UniSTS
Cytogenetic Map16p16UniSTS
RH127633  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01610,609,508 - 10,609,685NCBIRnor6.0
Rnor_6.02017,076,057 - 17,076,256NCBIRnor6.0
Rnor_5.02019,258,548 - 19,258,747UniSTSRnor5.0
Rnor_5.0168,928,049 - 8,928,226UniSTSRnor5.0
RGSC_v3.4169,911,823 - 9,912,000UniSTSRGSC3.4
Celera2017,366,620 - 17,366,819UniSTS
Cytogenetic Map16p16UniSTS
RH 3.4 Map20204.1UniSTS
RH134298  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01610,572,199 - 10,572,383NCBIRnor6.0
Rnor_5.0168,890,821 - 8,891,005UniSTSRnor5.0
RGSC_v3.4169,870,104 - 9,870,288UniSTSRGSC3.4
Celera165,665,560 - 5,665,744UniSTS
Cytogenetic Map16p16UniSTS
RH 3.4 Map1692.3UniSTS
AU047839  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01610,608,913 - 10,609,045NCBIRnor6.0
Rnor_5.0168,927,455 - 8,927,587UniSTSRnor5.0
RGSC_v3.4169,911,228 - 9,911,360UniSTSRGSC3.4
Celera165,628,880 - 5,629,006UniSTS
Cytogenetic Map16p16UniSTS
GDB:277890  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera165,575,880 - 5,576,138UniSTS
Cytogenetic Map16p16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16110660736Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16124228366Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16127556253Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16127556253Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16127556253Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16131816439Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16133160624Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16134465490Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16141240937Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16141240937Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16141240957Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)1624459345244593Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16134074146340741Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)16155018749247447Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16172829746728297Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16329668817464293Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16413635523105837Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16413635545905331Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380218360147Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16501380245905331Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380250013802Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16501380250169318Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16509870419398181Rat


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 1 49 39 17 39 5 26 19 10
Low 2 43 8 2 2 2 8 11 69 9 22 1 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001025028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771135 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771136 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771137 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07024658 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07072494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01086334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01086335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01086336 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC109685 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089872 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF420607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB613349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR474249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM098539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000085012   ⟹   ENSRNOP00000073233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1610,570,314 - 10,661,528 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087737   ⟹   ENSRNOP00000069549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1610,596,833 - 10,603,850 (-)Ensembl
RefSeq Acc Id: NM_001025028   ⟹   NP_001020199
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,661,528 (-)NCBI
Rnor_5.0168,888,929 - 8,979,969 (-)NCBI
RGSC_v3.4169,868,212 - 9,965,225 (-)RGD
Celera165,576,833 - 5,667,636 (+)RGD
Sequence:
RefSeq Acc Id: XM_008771135   ⟹   XP_008769357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,661,432 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771136   ⟹   XP_008769358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,661,432 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771137   ⟹   XP_008769359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,604,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771138   ⟹   XP_008769360
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,572,049 - 10,661,528 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600193   ⟹   XP_017455682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,661,432 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600194   ⟹   XP_017455683
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,661,432 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600195   ⟹   XP_017455684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,661,432 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600196   ⟹   XP_017455685
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,612,413 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600197   ⟹   XP_017455686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,661,432 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017600198   ⟹   XP_017455687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01610,570,307 - 10,613,507 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001020199   ⟸   NM_001025028
- UniProtKB: Q5FVM8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769358   ⟸   XM_008771136
- Peptide Label: isoform X1
- UniProtKB: D3ZH67 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769357   ⟸   XM_008771135
- Peptide Label: isoform X1
- UniProtKB: D3ZH67 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769359   ⟸   XM_008771137
- Peptide Label: isoform X1
- UniProtKB: D3ZH67 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769360   ⟸   XM_008771138
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017455683   ⟸   XM_017600194
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017455682   ⟸   XM_017600193
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017455684   ⟸   XM_017600195
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017455686   ⟸   XM_017600197
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017455687   ⟸   XM_017600198
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017455685   ⟸   XM_017600196
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000069549   ⟸   ENSRNOT00000087737
RefSeq Acc Id: ENSRNOP00000073233   ⟸   ENSRNOT00000085012
Protein Domains
FAM35_C

Transcriptome

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

Promoters
RGD ID:13699955
Promoter ID:EPDNEW_R10479
Type:initiation region
Name:Fam35a_1
Description:family with sequence similarity 35, member A
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_6.01610,661,539 - 10,661,599EPDNEW

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)
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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
BBDP/Wor (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
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)
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)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 10602965 10602966 T A snv F344/NRrrc (MCW), MR/N (MCW), M520/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565067 AgrOrtholog
Ensembl Genes ENSRNOG00000059057 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069549 UniProtKB/TrEMBL
  ENSRNOP00000073233 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000085012 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000087737 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7325236 IMAGE-MGC_LOAD
InterPro FAM35A UniProtKB/TrEMBL
  FAM35A_C UniProtKB/TrEMBL
KEGG Report rno:364514 UniProtKB/TrEMBL
MGC_CLONE MGC:109007 IMAGE-MGC_LOAD
NCBI Gene 364514 ENTREZGENE
PANTHER PTHR14495 UniProtKB/TrEMBL
Pfam FAM35_C UniProtKB/TrEMBL
PhenoGen Shld2 PhenoGen
UniGene Rn.28390 ENTREZGENE
UniProt A0A0G2JVN0_RAT UniProtKB/TrEMBL
  D3ZH67 ENTREZGENE, UniProtKB/TrEMBL
  Q5FVM8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-07 Shld2  shieldin complex subunit 2  Fam35a  family with sequence similarity 35, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Fam35a  family with sequence similarity 35, member A  LOC364514  hypothetical protein LOC364514  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC364514  hypothetical protein LOC364514      Symbol and Name status set to provisional 70820 PROVISIONAL