Scand1 (SCAN domain-containing 1) - Rat Genome Database

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Gene: Scand1 (SCAN domain-containing 1) Rattus norvegicus
Analyze
Symbol: Scand1
Name: SCAN domain-containing 1
RGD ID: 1308530
Description: Predicted to act upstream of or within positive regulation of DNA-templated transcription. Predicted to be located in nucleus. Orthologous to human SCAND1 (SCAN domain containing 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC362252; SCAN domain-containing protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83165,278,723 - 165,279,587 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3165,278,723 - 165,279,587 (-)EnsemblGRCr8
mRatBN7.23144,818,615 - 144,819,479 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3144,818,611 - 144,820,025 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3148,684,260 - 148,685,124 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03157,301,562 - 157,302,426 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03155,040,981 - 155,041,845 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03152,381,665 - 152,382,529 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3152,381,665 - 152,382,529 (-)Ensemblrn6Rnor6.0
Rnor_5.03159,308,252 - 159,309,116 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43146,710,153 - 146,711,017 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3143,540,334 - 143,541,198 (-)NCBICelera
RGSC_v3.13146,616,064 - 146,621,863 (-)NCBI
Cytogenetic Map3q42NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10393183  


Genomics

Comparative Map Data
Scand1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83165,278,723 - 165,279,587 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3165,278,723 - 165,279,587 (-)EnsemblGRCr8
mRatBN7.23144,818,615 - 144,819,479 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3144,818,611 - 144,820,025 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3148,684,260 - 148,685,124 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03157,301,562 - 157,302,426 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03155,040,981 - 155,041,845 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03152,381,665 - 152,382,529 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3152,381,665 - 152,382,529 (-)Ensemblrn6Rnor6.0
Rnor_5.03159,308,252 - 159,309,116 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43146,710,153 - 146,711,017 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3143,540,334 - 143,541,198 (-)NCBICelera
RGSC_v3.13146,616,064 - 146,621,863 (-)NCBI
Cytogenetic Map3q42NCBI
SCAND1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382035,953,624 - 35,959,472 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2035,953,617 - 35,959,472 (-)Ensemblhg38GRCh38
GRCh372034,541,546 - 34,547,394 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362034,004,960 - 34,005,842 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342034,004,959 - 34,005,842NCBI
Celera2031,289,831 - 31,290,713 (-)NCBICelera
Cytogenetic Map20q11.23NCBI
HuRef2031,319,340 - 31,321,082 (-)NCBIHuRef
CHM1_12034,443,519 - 34,445,261 (-)NCBICHM1_1
T2T-CHM13v2.02037,674,621 - 37,680,469 (-)NCBIT2T-CHM13v2.0
Scand1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392156,153,766 - 156,154,624 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2156,153,766 - 156,154,667 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm382156,311,846 - 156,312,704 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2156,311,846 - 156,312,747 (-)Ensemblmm10GRCm38
MGSCv372156,137,582 - 156,138,440 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362156,003,299 - 156,003,967 (-)NCBIMGSCv36mm8
Celera2162,248,159 - 162,249,017 (-)NCBICelera
Cytogenetic Map2H1NCBI
cM Map277.39NCBI
Scand1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542225,561,400 - 25,561,942 (+)Ensembl
ChiLan1.0NW_00495542225,561,146 - 25,562,042 (+)NCBIChiLan1.0ChiLan1.0
SCAND1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22141,691,623 - 41,693,350 (-)NCBINHGRI_mPanPan1-v2
SCAND1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12424,822,272 - 24,823,368 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2424,822,528 - 24,823,067 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2424,468,761 - 24,469,875 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02425,514,534 - 25,515,626 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2425,514,786 - 25,515,325 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12424,800,222 - 24,801,334 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02424,894,558 - 24,895,672 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02425,384,245 - 25,385,355 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Scand1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640173,795,040 - 173,795,967 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365614,953,874 - 4,954,401 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365614,953,653 - 4,954,636 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCAND1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1739,244,460 - 39,245,633 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11739,244,456 - 39,245,628 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21744,650,808 - 44,651,976 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCAND1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1256,813,371 - 56,814,367 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl256,813,492 - 56,814,328 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660873,297,669 - 3,298,684 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scand1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248423,509,640 - 3,510,179 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248423,509,334 - 3,510,281 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Scand1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v15135,661,055 - 135,661,917 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Scand1
3 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:78
Count of miRNA genes:67
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000027076
Prediction methods:Microtar, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3141555229186555229Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141555229186555229Rat
1582233Insul10Insulin level QTL 105.40.0015blood insulin amount (VT:0001560)serum insulin level times blood glucose level (CMO:0002040)3133259579178259579Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3141555229186555229Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3141555229186555229Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3129154923182114333Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3141555229186555229Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3141555229186555229Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161492708189428310Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161799493176036425Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3133134628178134628Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3161799270187311134Rat
1582213Insul6Insulin level QTL 63.70.0009blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3141508991166376254Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3142898802187898802Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)3145335553189428310Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3125116475170116475Rat
1582256Insul9Insulin level QTL 94.40.0016blood insulin amount (VT:0001560)absolute change in serum insulin level (CMO:0002038)3155759447189428310Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3139299381184299381Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3122395989167395989Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3141508991177728348Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)3131036586176036586Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3137114333182114333Rat
1582248Insul7Insulin level QTL 73.90.0041blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)3131036586176036586Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)398651826167012663Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3141555229186555229Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3160357340167835660Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 67 161 91 90 59 92 59 6 355 191 9 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000027076   ⟹   ENSRNOP00000061203
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3165,278,723 - 165,279,587 (-)Ensembl
mRatBN7.2 Ensembl3144,818,611 - 144,820,025 (-)Ensembl
Rnor_6.0 Ensembl3152,381,665 - 152,382,529 (-)Ensembl
RefSeq Acc Id: NM_001108599   ⟹   NP_001102069
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,278,723 - 165,279,587 (-)NCBI
mRatBN7.23144,818,615 - 144,819,479 (-)NCBI
Rnor_6.03152,381,665 - 152,382,529 (-)NCBI
Rnor_5.03159,308,252 - 159,309,116 (+)NCBI
RGSC_v3.43146,710,153 - 146,711,017 (-)RGD
Celera3143,540,334 - 143,541,198 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102069 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL85850 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000061203
  ENSRNOP00000061203.1
RefSeq Acc Id: NP_001102069   ⟸   NM_001108599
- UniProtKB: D4A6K0 (UniProtKB/TrEMBL),   A6KIA5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000061203   ⟸   ENSRNOT00000027076
Protein Domains
SCAN box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A6K0-F1-model_v2 AlphaFold D4A6K0 1-142 view protein structure

Transcriptome

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

Promoters
RGD ID:13692600
Promoter ID:EPDNEW_R3124
Type:multiple initiation site
Name:Scand1_1
Description:SCAN domain-containing 1
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_6.03152,382,346 - 152,382,406EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308530 AgrOrtholog
BioCyc Gene G2FUF-47100 BioCyc
Ensembl Genes ENSRNOG00000019987 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027076 ENTREZGENE
  ENSRNOT00000027076.5 UniProtKB/TrEMBL
Gene3D-CATH 1.10.4020.10 UniProtKB/TrEMBL
InterPro SCAN-C2H2_zinc_finger UniProtKB/TrEMBL
  SCAN_sf UniProtKB/TrEMBL
  Tscrpt_reg_SCAN UniProtKB/TrEMBL
KEGG Report rno:362252 UniProtKB/TrEMBL
NCBI Gene 362252 ENTREZGENE
PANTHER PROTEIN ZBED8-RELATED UniProtKB/TrEMBL
  SCAN DOMAIN-CONTAINING 1 UniProtKB/TrEMBL
Pfam SCAN UniProtKB/TrEMBL
PhenoGen Scand1 PhenoGen
PROSITE SCAN_BOX UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019987 RatGTEx
SMART SCAN UniProtKB/TrEMBL
Superfamily-SCOP Retrovirus capsid dimerization domain-like UniProtKB/TrEMBL
UniProt A6KIA5 ENTREZGENE, UniProtKB/TrEMBL
  D4A6K0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Scand1  SCAN domain-containing 1   Scand1_predicted  SCAN domain-containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Scand1_predicted  SCAN domain-containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED