RETREG3 (reticulophagy regulator family member 3) - Rat Genome Database

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Gene: RETREG3 (reticulophagy regulator family member 3) Canis lupus familiaris
Analyze
Symbol: RETREG3
Name: reticulophagy regulator family member 3
RGD ID: 12244713
Description: ENCODES a protein that exhibits endoplasmic reticulum-autophagosome adaptor activity (inferred); INVOLVED IN collagen catabolic process (ortholog); endoplasmic reticulum organization (ortholog); reticulophagy (ortholog); ASSOCIATED WITH genetic disease (ortholog); FOUND IN endoplasmic reticulum (inferred); endoplasmic reticulum membrane (inferred); endoplasmic reticulum tubular network (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: FAM134C; family with sequence similarity 134 member C; protein FAM134C; reticulophagy regulator 3
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1920,363,729 - 20,385,580 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl920,363,823 - 20,385,592 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha919,825,556 - 19,847,433 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0921,082,652 - 21,104,534 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl921,082,776 - 21,102,778 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1919,868,516 - 19,890,379 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0920,133,752 - 20,155,605 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0920,237,775 - 20,259,647 (+)NCBIUU_Cfam_GSD_1.0
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:30032202  


Genomics

Comparative Map Data
RETREG3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1920,363,729 - 20,385,580 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl920,363,823 - 20,385,592 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha919,825,556 - 19,847,433 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0921,082,652 - 21,104,534 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl921,082,776 - 21,102,778 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1919,868,516 - 19,890,379 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0920,133,752 - 20,155,605 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0920,237,775 - 20,259,647 (+)NCBIUU_Cfam_GSD_1.0
RETREG3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381742,579,508 - 42,609,427 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1742,579,513 - 42,610,623 (-)EnsemblGRCh38hg38GRCh38
GRCh371740,731,526 - 40,761,445 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361737,985,059 - 38,014,928 (-)NCBINCBI36Build 36hg18NCBI36
Celera1737,387,436 - 37,417,341 (-)NCBICelera
Cytogenetic Map17q21.2NCBI
HuRef1736,496,172 - 36,526,037 (-)NCBIHuRef
CHM1_11740,967,335 - 40,997,209 (-)NCBICHM1_1
T2T-CHM13v2.01743,436,673 - 43,466,572 (-)NCBIT2T-CHM13v2.0
Retreg3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911100,987,148 - 101,010,720 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11100,987,148 - 101,010,719 (-)EnsemblGRCm39 Ensembl
GRCm3811101,096,322 - 101,119,841 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11101,096,322 - 101,119,893 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711100,957,636 - 100,981,157 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611100,912,412 - 100,935,933 (-)NCBIMGSCv36mm8
Celera11112,392,424 - 112,415,945 (-)NCBICelera
Cytogenetic Map11DNCBI
cM Map1164.2NCBI
Retreg3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81086,529,048 - 86,552,873 (-)NCBIGRCr8
mRatBN7.21086,028,767 - 86,052,575 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1086,028,774 - 86,052,692 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1091,065,276 - 91,089,086 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01090,544,049 - 90,567,863 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01085,937,216 - 85,961,025 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01089,006,595 - 89,030,595 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1089,006,595 - 89,030,595 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01088,805,091 - 88,829,091 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41090,113,395 - 90,137,543 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1084,746,462 - 84,770,275 (-)NCBICelera
Cytogenetic Map10q31NCBI
Retreg3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545116,468,845 - 16,486,773 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545116,468,845 - 16,486,773 (-)NCBIChiLan1.0ChiLan1.0
RETREG3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21922,375,425 - 22,405,094 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11724,265,580 - 24,295,083 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01714,707,649 - 14,737,027 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11714,931,260 - 14,958,511 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1714,931,260 - 14,958,511 (+)Ensemblpanpan1.1panPan2
Retreg3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560219,717,594 - 19,739,965 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649017,334,464 - 17,357,570 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649017,334,458 - 17,357,544 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RETREG3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1220,179,078 - 20,243,293 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11220,220,993 - 20,243,299 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21220,433,577 - 20,456,000 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RETREG3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11663,680,831 - 63,708,160 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1663,680,890 - 63,710,015 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607734,474,127 - 34,503,820 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Retreg3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247951,516,315 - 1,535,162 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247951,516,339 - 1,535,162 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RETREG3
165 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 circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 5 22 6 6 6 6 12 8 10 6
Low 5 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000049798   ⟹   ENSCAFP00000037083
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl920,363,823 - 20,385,592 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845014960   ⟹   ENSCAFP00845011599
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl921,082,776 - 21,102,778 (+)Ensembl
RefSeq Acc Id: XM_038485499   ⟹   XP_038341427
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1919,868,516 - 19,890,379 (+)NCBI
RefSeq Acc Id: XM_038547261   ⟹   XP_038403189
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0920,237,775 - 20,259,647 (+)NCBI
RefSeq Acc Id: XM_038611230   ⟹   XP_038467158
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0920,133,752 - 20,155,605 (+)NCBI
RefSeq Acc Id: XM_038676418   ⟹   XP_038532346
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0921,082,652 - 21,104,534 (+)NCBI
RefSeq Acc Id: XM_548087   ⟹   XP_548087
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1920,363,729 - 20,385,580 (+)NCBI
Dog10K_Boxer_Tasha919,825,556 - 19,847,433 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_548087   ⟸   XM_548087
- UniProtKB: A0A8C0KJS9 (UniProtKB/TrEMBL),   A0A8C0QJ10 (UniProtKB/TrEMBL),   A0A8I3MY43 (UniProtKB/TrEMBL),   A0A8C0M050 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000037083   ⟸   ENSCAFT00000049798
RefSeq Acc Id: XP_038341427   ⟸   XM_038485499
RefSeq Acc Id: XP_038467158   ⟸   XM_038611230
RefSeq Acc Id: XP_038532346   ⟸   XM_038676418
- UniProtKB: A0A8C0KJS9 (UniProtKB/TrEMBL),   A0A8C0QJ10 (UniProtKB/TrEMBL),   A0A8I3MY43 (UniProtKB/TrEMBL),   A0A8C0M050 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038403189   ⟸   XM_038547261
- UniProtKB: A0A8C0KJS9 (UniProtKB/TrEMBL),   A0A8C0M050 (UniProtKB/TrEMBL),   A0A8C0QJ10 (UniProtKB/TrEMBL),   A0A8I3MY43 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845011599   ⟸   ENSCAFT00845014960

Promoters
RGD ID:13684516
Promoter ID:EPDNEW_C2583
Type:initiation region
Name:RETREG3_1
Description:reticulophagy regulator family member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1920,363,782 - 20,363,842EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000014921 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030000948 UniProtKB/TrEMBL
  ENSCAFG00040007553 UniProtKB/TrEMBL
  ENSCAFG00845008519 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000049798.3 UniProtKB/TrEMBL
  ENSCAFT00030001665.1 UniProtKB/TrEMBL
  ENSCAFT00040014064.1 UniProtKB/TrEMBL
  ENSCAFT00845014960 ENTREZGENE
  ENSCAFT00845014960.1 UniProtKB/TrEMBL
InterPro RETREG1/3 UniProtKB/TrEMBL
KEGG Report cfa:490964 UniProtKB/TrEMBL
NCBI Gene FAM134C ENTREZGENE
PANTHER PTHR28659 UniProtKB/TrEMBL
  PTHR28659:SF1 UniProtKB/TrEMBL
UniProt A0A8C0KJS9 ENTREZGENE
  A0A8C0M050 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0QJ10 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3MY43 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:45485 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 RETREG3  reticulophagy regulator family member 3  FAM134C  family with sequence similarity 134 member C  Symbol and/or name change 5135510 APPROVED