SCGN (secretagogin, EF-hand calcium binding protein) - Rat Genome Database

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Gene: SCGN (secretagogin, EF-hand calcium binding protein) Sus scrofa
Analyze
Symbol: SCGN
Name: secretagogin, EF-hand calcium binding protein
RGD ID: 13855766
Description: ENCODES a protein that exhibits calcium ion binding (inferred); metal ion binding (inferred); INVOLVED IN regulation of long-term synaptic potentiation (inferred); regulation of presynaptic cytosolic calcium ion concentration (inferred); FOUND IN cytoplasm (inferred); cytoplasmic vesicle (inferred); cytosol (inferred); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: secretagogin
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl720,389,493 - 20,432,978 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1720,389,156 - 20,432,985 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2721,689,440 - 21,732,931 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IEA)
cytoplasmic vesicle  (IEA)
cytosol  (IBA,IEA)
dendrite  (IBA,IEA)
extracellular region  (IEA)
membrane  (IEA)
nucleus  (IBA,IEA)
synapse  (IBA,IEA)
terminal bouton  (IBA,IEA)
transport vesicle membrane  (IEA)

Molecular Function

References
Additional References at PubMed
PMID:14681463   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SCGN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl720,389,493 - 20,432,978 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1720,389,156 - 20,432,985 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2721,689,440 - 21,732,931 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SCGN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38625,652,215 - 25,701,783 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl625,652,201 - 25,701,783 (+)EnsemblGRCh38hg38GRCh38
GRCh37625,652,443 - 25,702,011 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36625,760,408 - 25,809,990 (+)NCBINCBI36Build 36hg18NCBI36
Build 34625,760,407 - 25,809,985NCBI
Celera626,879,633 - 26,929,216 (+)NCBICelera
Cytogenetic Map6p22.2NCBI
HuRef625,595,416 - 25,644,987 (+)NCBIHuRef
CHM1_1625,654,627 - 25,704,213 (+)NCBICHM1_1
T2T-CHM13v2.0625,518,025 - 25,567,550 (+)NCBIT2T-CHM13v2.0
Scgn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391324,137,439 - 24,175,310 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1324,137,439 - 24,175,197 (-)EnsemblGRCm39 Ensembl
GRCm381323,953,456 - 23,991,327 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,953,456 - 23,991,214 (-)EnsemblGRCm38mm10GRCm38
MGSCv371324,045,325 - 24,083,083 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361323,960,921 - 23,998,679 (-)NCBIMGSCv36mm8
Celera1324,185,142 - 24,222,913 (-)NCBICelera
Cytogenetic Map13A3.1NCBI
cM Map1310.01NCBI
Scgn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81741,534,558 - 41,576,525 (+)NCBIGRCr8
mRatBN7.21741,106,681 - 41,148,656 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1741,106,467 - 41,148,667 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1741,174,261 - 41,215,631 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01742,778,305 - 42,819,675 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01741,062,609 - 41,103,976 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01743,357,888 - 43,399,321 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,357,888 - 43,399,321 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01745,214,579 - 45,256,809 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41748,225,075 - 48,266,508 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11748,227,915 - 48,269,349 (+)NCBI
Celera1740,739,598 - 40,779,916 (+)NCBICelera
Cytogenetic Map17p11NCBI
Scgn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554831,392,770 - 1,429,594 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554831,392,772 - 1,429,563 (-)NCBIChiLan1.0ChiLan1.0
SCGN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2540,299,097 - 40,367,239 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1636,300,454 - 36,350,030 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0625,486,599 - 25,571,272 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1625,812,650 - 25,862,236 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl625,812,443 - 25,862,227 (+)Ensemblpanpan1.1panPan2
SCGN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13523,602,244 - 23,638,108 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3523,602,343 - 23,638,055 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3523,531,684 - 23,540,559 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03523,717,908 - 23,753,767 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3523,717,868 - 23,753,765 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13523,527,247 - 23,563,304 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03523,577,972 - 23,614,023 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03525,015,623 - 25,051,501 (+)NCBIUU_Cfam_GSD_1.0
Scgn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049461,929,640 - 1,965,364 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366711,655,978 - 1,693,175 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366711,656,179 - 1,696,580 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCGN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11746,554,759 - 46,605,282 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1746,565,302 - 46,604,710 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604425,585,367 - 25,635,700 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scgn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247561,368,434 - 1,407,885 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247561,368,330 - 1,407,914 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SCGN
1724 total Variants

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 endocrine system hemolymphoid system nervous system renal system reproductive system respiratory system
High
Medium
Low 5 3 9 2
Below cutoff 3 1 4 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000001197   ⟹   ENSSSCP00000001171
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl720,389,493 - 20,432,978 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000087451   ⟹   ENSSSCP00000061584
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl720,389,493 - 20,432,978 (+)Ensembl
RefSeq Acc Id: NM_001077224   ⟹   NP_001070692
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1720,389,726 - 20,432,535 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005665639   ⟹   XP_005665696
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1720,389,156 - 20,432,985 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_005665696   ⟸   XM_005665639
- Peptide Label: isoform X1
- UniProtKB: A0A8D0U6W3 (UniProtKB/TrEMBL),   A0A8D1CB08 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001070692   ⟸   NM_001077224
- UniProtKB: Q06A97 (UniProtKB/Swiss-Prot),   A0A8D0U6W3 (UniProtKB/TrEMBL),   A0A8D1CB08 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000001171   ⟸   ENSSSCT00000001197
RefSeq Acc Id: ENSSSCP00000061584   ⟸   ENSSSCT00000087451
Protein Domains
EF-hand


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000001101 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSSSCG00005006329 UniProtKB/TrEMBL
  ENSSSCG00015055906 UniProtKB/TrEMBL
  ENSSSCG00025022235 UniProtKB/TrEMBL
  ENSSSCG00030049488 UniProtKB/TrEMBL
  ENSSSCG00035078561 UniProtKB/Swiss-Prot
  ENSSSCG00040034100 UniProtKB/TrEMBL
  ENSSSCG00045007180 UniProtKB/Swiss-Prot
  ENSSSCG00050041939 UniProtKB/TrEMBL
  ENSSSCG00055027232 UniProtKB/TrEMBL
  ENSSSCG00060026507 UniProtKB/TrEMBL
  ENSSSCG00065046234 UniProtKB/Swiss-Prot
  ENSSSCG00070025043 UniProtKB/Swiss-Prot
Ensembl Transcript ENSSSCT00000001197 ENTREZGENE
  ENSSSCT00000001197.3 UniProtKB/Swiss-Prot
  ENSSSCT00000087451 ENTREZGENE
  ENSSSCT00000087451.1 UniProtKB/TrEMBL
  ENSSSCT00005009734.1 UniProtKB/TrEMBL
  ENSSSCT00015074723.1 UniProtKB/TrEMBL
  ENSSSCT00025030258.1 UniProtKB/TrEMBL
  ENSSSCT00030069032.1 UniProtKB/TrEMBL
  ENSSSCT00035107283.1 UniProtKB/Swiss-Prot
  ENSSSCT00040045944.1 UniProtKB/TrEMBL
  ENSSSCT00045011931.1 UniProtKB/Swiss-Prot
  ENSSSCT00050056973.1 UniProtKB/TrEMBL
  ENSSSCT00055053872.1 UniProtKB/TrEMBL
  ENSSSCT00060035878.1 UniProtKB/TrEMBL
  ENSSSCT00065063223.1 UniProtKB/Swiss-Prot
  ENSSSCT00070050059.1 UniProtKB/Swiss-Prot
Gene3D-CATH EF-hand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EFh_SCGN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report ssc:768111 UniProtKB/Swiss-Prot
NCBI Gene SCGN ENTREZGENE
PANTHER CALBINDIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SECRETAGOGIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EF-hand_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand_7 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EFh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A5G2QC00_PIG UniProtKB/TrEMBL
  A0A8D0U6W3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1CB08 ENTREZGENE, UniProtKB/TrEMBL
  Q06A97 ENTREZGENE, UniProtKB/Swiss-Prot
VGNC ID VGNC:92624 ENTREZGENE