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

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Gene: TLCD3A (TLC domain containing 3A) Canis lupus familiaris
Analyze
Symbol: TLCD3A
Name: TLC domain containing 3A
RGD ID: 12176057
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; TLC domain-containing protein 3A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
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

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
59 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 13 6 9 8 10 5
Low 5 9 6 6 6 6 3 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_022423440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038486584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038486585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038548441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038548442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038612379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038612380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038677655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038677656 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_537761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005331053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005364751 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005399190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005432521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_293216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000030379   ⟹   ENSCAFP00000028226
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl945,048,687 - 45,056,049 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000044283   ⟹   ENSCAFP00000037821
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl945,048,510 - 45,056,049 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000067621   ⟹   ENSCAFP00000058928
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl945,048,953 - 45,056,049 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024468   ⟹   ENSCAFP00845019242
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl945,865,781 - 45,874,570 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024488   ⟹   ENSCAFP00845019262
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl945,867,189 - 45,874,570 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024499   ⟹   ENSCAFP00845019271
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl945,867,455 - 45,874,570 (-)Ensembl
RefSeq Acc Id: XM_022423440   ⟹   XP_022279148
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1945,049,465 - 45,056,069 (-)NCBI
Dog10K_Boxer_Tasha944,199,992 - 44,206,684 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038486584   ⟹   XP_038342512
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1944,644,213 - 44,653,057 (-)NCBI
RefSeq Acc Id: XM_038486585   ⟹   XP_038342513
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1944,646,403 - 44,653,097 (-)NCBI
RefSeq Acc Id: XM_038548441   ⟹   XP_038404369
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0945,016,456 - 45,025,323 (-)NCBI
RefSeq Acc Id: XM_038548442   ⟹   XP_038404370
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0945,018,648 - 45,025,363 (-)NCBI
RefSeq Acc Id: XM_038612379   ⟹   XP_038468307
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0944,937,927 - 44,946,772 (-)NCBI
RefSeq Acc Id: XM_038612380   ⟹   XP_038468308
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0944,940,116 - 44,946,812 (-)NCBI
RefSeq Acc Id: XM_038677655   ⟹   XP_038533583
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0945,865,775 - 45,874,633 (-)NCBI
RefSeq Acc Id: XM_038677656   ⟹   XP_038533584
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0945,867,967 - 45,874,673 (-)NCBI
RefSeq Acc Id: XM_537761   ⟹   XP_537761
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1945,047,286 - 45,056,069 (-)NCBI
Dog10K_Boxer_Tasha944,197,799 - 44,206,644 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005331053
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1944,644,213 - 44,653,057 (-)NCBI
RefSeq Acc Id: XR_005364751
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0945,016,456 - 45,025,323 (-)NCBI
RefSeq Acc Id: XR_005399190
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0944,937,927 - 44,946,772 (-)NCBI
RefSeq Acc Id: XR_005432521
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0945,865,775 - 45,874,633 (-)NCBI
RefSeq Acc Id: XR_293216
Type: NON-CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1945,047,286 - 45,056,069 (-)NCBI
Dog10K_Boxer_Tasha944,197,799 - 44,206,644 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_537761   ⟸   XM_537761
- Peptide Label: isoform X1
- UniProtKB: A0A8C0NRQ6 (UniProtKB/TrEMBL),   A0A8I3NT92 (UniProtKB/TrEMBL),   A0A8C0Q8Q5 (UniProtKB/TrEMBL),   A0A8I3P0S0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022279148   ⟸   XM_022423440
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSCAFP00000028226   ⟸   ENSCAFT00000030379
RefSeq Acc Id: ENSCAFP00000058928   ⟸   ENSCAFT00000067621
RefSeq Acc Id: ENSCAFP00000037821   ⟸   ENSCAFT00000044283
RefSeq Acc Id: XP_038342512   ⟸   XM_038486584
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038342513   ⟸   XM_038486585
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038468307   ⟸   XM_038612379
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038468308   ⟸   XM_038612380
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038533583   ⟸   XM_038677655
- Peptide Label: isoform X1
- UniProtKB: A0A8C0NRQ6 (UniProtKB/TrEMBL),   A0A8I3NT92 (UniProtKB/TrEMBL),   A0A8C0Q8Q5 (UniProtKB/TrEMBL),   A0A8I3P0S0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038533584   ⟸   XM_038677656
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038404369   ⟸   XM_038548441
- Peptide Label: isoform X1
- UniProtKB: A0A8C0NRQ6 (UniProtKB/TrEMBL),   A0A8C0Q8Q5 (UniProtKB/TrEMBL),   A0A8I3NT92 (UniProtKB/TrEMBL),   A0A8I3P0S0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038404370   ⟸   XM_038548442
- Peptide Label: isoform X2
RefSeq Acc Id: ENSCAFP00845019271   ⟸   ENSCAFT00845024499
RefSeq Acc Id: ENSCAFP00845019242   ⟸   ENSCAFT00845024468
RefSeq Acc Id: ENSCAFP00845019262   ⟸   ENSCAFT00845024488
Protein Domains
TLC

Promoters
RGD ID:13684704
Promoter ID:EPDNEW_C2772
Type:multiple initiation site
Name:FAM57A_1
Description:family with sequence similarity 57 member A
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
CanFam3.1945,055,999 - 45,056,059EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000019129 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030016353 UniProtKB/TrEMBL
  ENSCAFG00040002191 UniProtKB/TrEMBL
  ENSCAFG00845013713 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000030379.5 UniProtKB/TrEMBL
  ENSCAFT00000044283.4 UniProtKB/TrEMBL
  ENSCAFT00000067621.2 UniProtKB/TrEMBL
  ENSCAFT00030030148.1 UniProtKB/TrEMBL
  ENSCAFT00030030202.1 UniProtKB/TrEMBL
  ENSCAFT00030030219.1 UniProtKB/TrEMBL
  ENSCAFT00040004161.1 UniProtKB/TrEMBL
  ENSCAFT00040004164.1 UniProtKB/TrEMBL
  ENSCAFT00040004175.1 UniProtKB/TrEMBL
  ENSCAFT00845024468 ENTREZGENE
  ENSCAFT00845024468.1 UniProtKB/TrEMBL
  ENSCAFT00845024488.1 UniProtKB/TrEMBL
  ENSCAFT00845024499.1 UniProtKB/TrEMBL
InterPro TLC-dom 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 A0A8C0NFJ8_CANLF UniProtKB/TrEMBL
  A0A8C0NRQ6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0Q8Q5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NRY9_CANLF UniProtKB/TrEMBL
  A0A8I3NT92 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3P0S0 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:40690 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-05-14 TLCD3A  TLC domain containing 3A  FAM57A  family with sequence similarity 57 member A  Symbol and/or name change 5135510 APPROVED