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); 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


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