TLCD3A (TLC domain containing 3A) - Rat Genome Database

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Gene: TLCD3A (TLC domain containing 3A) Sus scrofa
Analyze
Symbol: TLCD3A
Name: TLC domain containing 3A
RGD ID: 14169664
Description: INVOLVED IN lipid homeostasis (inferred); ASSOCIATED WITH Fraser syndrome 3 (ortholog); genetic disease (ortholog); FOUND IN endoplasmic reticulum (inferred); membrane (inferred); plasma membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: FAM57A; family with sequence similarity 57 member A; protein FAM57A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1247,116,565 - 47,125,099 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11247,116,523 - 47,125,523 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21249,280,815 - 49,289,294 (-)NCBISscrofa10.2Sscrofa10.2susScr3
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

Biological Process
lipid homeostasis  (IBA,IEA)

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
TLCD3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1247,116,565 - 47,125,099 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11247,116,523 - 47,125,523 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21249,280,815 - 49,289,294 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TLCD3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3817732,596 - 742,968 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl17732,412 - 742,968 (+)EnsemblGRCh38hg38GRCh38
GRCh3717635,836 - 646,208 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3617582,597 - 592,825 (+)NCBINCBI36Build 36hg18NCBI36
Celera17647,932 - 658,167 (+)NCBICelera
Cytogenetic Map17p13.3NCBI
HuRef17546,800 - 557,045 (+)NCBIHuRef
CHM1_117644,640 - 654,872 (+)NCBICHM1_1
T2T-CHM13v2.017617,519 - 628,045 (+)NCBIT2T-CHM13v2.0
Tlcd3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391176,070,497 - 76,100,243 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1176,070,497 - 76,105,653 (+)EnsemblGRCm39 Ensembl
GRCm381176,179,671 - 76,209,417 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1176,179,671 - 76,214,827 (+)EnsemblGRCm38mm10GRCm38
MGSCv371176,015,558 - 76,021,759 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361175,995,866 - 76,025,812 (+)NCBIMGSCv36mm8
Celera1183,714,742 - 83,720,938 (+)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1145.92NCBI
Tlcd3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81061,556,193 - 61,563,529 (+)NCBIGRCr8
mRatBN7.21061,057,470 - 61,065,293 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1061,058,042 - 61,065,283 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1065,700,501 - 65,707,684 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01065,205,949 - 65,213,132 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01060,676,375 - 60,683,604 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01064,360,374 - 64,367,679 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1064,360,390 - 64,366,586 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01063,646,620 - 63,655,443 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.11063,569,371 - 63,575,904 (+)NCBI
Celera1060,073,418 - 60,080,681 (+)NCBICelera
Cytogenetic Map10q24NCBI
Tlcd3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554812,283,620 - 2,291,352 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554812,283,620 - 2,292,100 (+)NCBIChiLan1.0ChiLan1.0
TLCD3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2198,281,755 - 8,292,564 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1179,831,334 - 9,841,907 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v017701,573 - 712,259 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.117626,044 - 636,033 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl17626,175 - 634,640 (+)Ensemblpanpan1.1panPan2
TLCD3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1945,047,286 - 45,056,069 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl945,048,510 - 45,056,049 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha944,197,799 - 44,206,684 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0945,865,775 - 45,874,673 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl945,865,781 - 45,874,570 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1944,644,213 - 44,653,097 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0944,937,927 - 44,946,812 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0945,016,456 - 45,025,363 (-)NCBIUU_Cfam_GSD_1.0
Tlcd3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560244,157,832 - 44,189,341 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365387,041,973 - 7,049,432 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365387,038,799 - 7,049,428 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TLCD3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.116483,303 - 493,238 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605921,592,724 - 21,603,547 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tlcd3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247863,566,561 - 3,575,449 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247863,564,938 - 3,575,478 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in TLCD3A
289 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 hemolymphoid system nervous system renal system reproductive system respiratory system
High
Medium
Low 2 1 10
Below cutoff 8 3 2 4 13 2 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000019383   ⟹   ENSSSCP00000018869
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1247,116,565 - 47,125,022 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000058531   ⟹   ENSSSCP00000032434
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1247,116,936 - 47,125,099 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000067662   ⟹   ENSSSCP00000059992
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1247,118,203 - 47,125,099 (-)Ensembl
RefSeq Acc Id: XM_003131817   ⟹   XP_003131865
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11247,116,523 - 47,125,523 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021067531   ⟹   XP_020923190
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11247,118,689 - 47,125,523 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_003131865   ⟸   XM_003131817
- Peptide Label: isoform X1
- UniProtKB: F1RHJ6 (UniProtKB/TrEMBL),   A0A8D1PDB0 (UniProtKB/TrEMBL),   A0A8D1VWN0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020923190   ⟸   XM_021067531
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSSSCP00000032434   ⟸   ENSSSCT00000058531
RefSeq Acc Id: ENSSSCP00000018869   ⟸   ENSSSCT00000019383
RefSeq Acc Id: ENSSSCP00000059992   ⟸   ENSSSCT00000067662
Protein Domains
TLC


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000017810 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00025073275 UniProtKB/TrEMBL
  ENSSSCG00035066148 UniProtKB/TrEMBL
  ENSSSCG00055000639 UniProtKB/TrEMBL
  ENSSSCG00060051649 UniProtKB/TrEMBL
  ENSSSCG00065076803 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000019383 ENTREZGENE
  ENSSSCT00000019383.4 UniProtKB/TrEMBL
  ENSSSCT00000058531.3 UniProtKB/TrEMBL
  ENSSSCT00000067662.2 UniProtKB/TrEMBL
  ENSSSCT00025100919.1 UniProtKB/TrEMBL
  ENSSSCT00035089107.1 UniProtKB/TrEMBL
  ENSSSCT00055001134.1 UniProtKB/TrEMBL
  ENSSSCT00060070305.1 UniProtKB/TrEMBL
  ENSSSCT00065106166.1 UniProtKB/TrEMBL
InterPro TLC-dom UniProtKB/TrEMBL
KEGG Report ssc:100524042 UniProtKB/TrEMBL
NCBI Gene FAM57A ENTREZGENE
PANTHER CT120 PROTEIN UniProtKB/TrEMBL
  TLC DOMAIN-CONTAINING PROTEIN 3A UniProtKB/TrEMBL
Pfam TRAM_LAG1_CLN8 UniProtKB/TrEMBL
PROSITE TLC UniProtKB/TrEMBL
SMART TLC UniProtKB/TrEMBL
UniProt A0A286ZLU8_PIG UniProtKB/TrEMBL
  A0A5G2QNX3_PIG UniProtKB/TrEMBL
  A0A8D1PDB0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1VWN0 ENTREZGENE, UniProtKB/TrEMBL
  F1RHJ6 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:94012 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-05-07 TLCD3A  TLC domain containing 3A  FAM57A  family with sequence similarity 57 member A  Symbol and/or name change 5135510 APPROVED