IFT20 (intraflagellar transport 20) - Rat Genome Database

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Gene: IFT20 (intraflagellar transport 20) Canis lupus familiaris
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Symbol: IFT20
Name: intraflagellar transport 20
RGD ID: 12307164
Description: ENCODES a protein that exhibits opsin binding (inferred); small GTPase binding (inferred); INVOLVED IN cardiac muscle cell differentiation (ortholog); centrosome localization (ortholog); cilium assembly (ortholog); FOUND IN intraciliary transport particle B (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: intraflagellar transport 20 homolog; intraflagellar transport protein 20 homolog
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
CanFam3.1942,581,117 - 42,587,830 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl942,581,433 - 42,587,804 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha941,738,040 - 41,744,762 (-)NCBI
ROS_Cfam_1.0943,400,250 - 43,406,984 (-)NCBI
ROS_Cfam_1.0 Ensembl943,400,253 - 43,406,956 (-)Ensembl
UMICH_Zoey_3.1942,184,523 - 42,191,233 (-)NCBI
UNSW_CanFamBas_1.0942,475,746 - 42,482,460 (-)NCBI
UU_Cfam_GSD_1.0942,552,794 - 42,559,508 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

Genomics

Comparative Map Data
IFT20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1942,581,117 - 42,587,830 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl942,581,433 - 42,587,804 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha941,738,040 - 41,744,762 (-)NCBI
ROS_Cfam_1.0943,400,250 - 43,406,984 (-)NCBI
ROS_Cfam_1.0 Ensembl943,400,253 - 43,406,956 (-)Ensembl
UMICH_Zoey_3.1942,184,523 - 42,191,233 (-)NCBI
UNSW_CanFamBas_1.0942,475,746 - 42,482,460 (-)NCBI
UU_Cfam_GSD_1.0942,552,794 - 42,559,508 (-)NCBI
IFT20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381728,328,326 - 28,335,472 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1728,328,325 - 28,335,489 (-)EnsemblGRCh38hg38GRCh38
GRCh371726,655,352 - 26,662,498 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361723,679,480 - 23,686,622 (-)NCBINCBI36hg18NCBI36
Celera1723,517,095 - 23,524,237 (-)NCBI
Cytogenetic Map17q11.2NCBI
HuRef1722,863,745 - 22,870,909 (-)NCBIHuRef
CHM1_11726,718,244 - 26,725,407 (-)NCBICHM1_1
T2T-CHM13v2.01729,270,174 - 29,277,320 (-)NCBI
Ift20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391178,427,187 - 78,432,558 (+)NCBIGRCm39mm39
GRCm39 Ensembl1178,427,187 - 78,432,563 (+)Ensembl
GRCm381178,536,361 - 78,541,732 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1178,536,361 - 78,541,737 (+)EnsemblGRCm38mm10GRCm38
MGSCv371178,349,938 - 78,354,975 (+)NCBIGRCm37mm9NCBIm37
MGSCv361178,352,631 - 78,357,668 (+)NCBImm8
Celera1188,168,509 - 88,173,546 (+)NCBICelera
Cytogenetic Map11B5NCBI
Ift20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21063,432,597 - 63,438,125 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1063,432,633 - 63,438,124 (+)Ensembl
Rnor_6.01065,805,808 - 65,811,353 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1065,805,860 - 65,811,351 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01065,832,267 - 65,837,794 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41064,647,046 - 64,652,537 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11064,660,751 - 64,665,876 (+)NCBI
Celera1062,409,186 - 62,414,668 (+)NCBICelera
Cytogenetic Map10q25NCBI
Ift20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554814,799,548 - 4,807,751 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554814,799,548 - 4,807,751 (+)NCBIChiLan1.0ChiLan1.0
IFT20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11728,941,303 - 28,948,129 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1728,941,303 - 28,948,129 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01728,438,960 - 28,446,113 (+)NCBIMhudiblu_PPA_v0panPan3
Ift20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560241,603,943 - 41,613,893 (-)NCBI
SpeTri2.0NW_0049365384,484,484 - 4,491,688 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IFT20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1244,609,586 - 44,616,669 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11244,609,586 - 44,616,685 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21246,522,079 - 46,529,162 (-)NCBISscrofa10.2Sscrofa10.2susScr3
IFT20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11622,094,383 - 22,102,234 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660758,026,450 - 8,034,181 (+)NCBIVero_WHO_p1.0
Ift20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624786928,123 - 939,515 (-)NCBIHetGla_female_1.0hetGla2


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 5 21 5 6 5 6 3 12 8 10 6
Low 1 1 1 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_003435305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038486385 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038486386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038486387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038548223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038548224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038548225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038610490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038612188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038612189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038612190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038677445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038677447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038677448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_537740 (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: ENSCAFT00000029619   ⟹   ENSCAFP00000027528
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl942,581,433 - 42,587,804 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000071964   ⟹   ENSCAFP00000060249
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl942,581,535 - 42,587,804 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845027301   ⟹   ENSCAFP00845021485
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl943,400,253 - 43,406,956 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845027318   ⟹   ENSCAFP00845021499
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl943,400,671 - 43,406,956 (-)Ensembl
RefSeq Acc Id: XM_003435305   ⟹   XP_003435353
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1942,581,117 - 42,587,828 (-)NCBI
Dog10K_Boxer_Tasha941,738,040 - 41,744,760 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038486385   ⟹   XP_038342313
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1942,184,523 - 42,191,232 (-)NCBI
RefSeq Acc Id: XM_038486386   ⟹   XP_038342314
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1942,184,523 - 42,191,231 (-)NCBI
RefSeq Acc Id: XM_038486387   ⟹   XP_038342315
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1942,184,523 - 42,191,233 (-)NCBI
RefSeq Acc Id: XM_038548223   ⟹   XP_038404151
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0942,552,794 - 42,559,507 (-)NCBI
RefSeq Acc Id: XM_038548224   ⟹   XP_038404152
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0942,552,794 - 42,559,506 (-)NCBI
RefSeq Acc Id: XM_038548225   ⟹   XP_038404153
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0942,552,794 - 42,559,508 (-)NCBI
RefSeq Acc Id: XM_038610490   ⟹   XP_038466418
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha941,738,040 - 41,744,762 (-)NCBI
RefSeq Acc Id: XM_038612188   ⟹   XP_038468116
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0942,475,746 - 42,482,459 (-)NCBI
RefSeq Acc Id: XM_038612189   ⟹   XP_038468117
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0942,475,746 - 42,482,458 (-)NCBI
RefSeq Acc Id: XM_038612190   ⟹   XP_038468118
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0942,475,746 - 42,482,460 (-)NCBI
RefSeq Acc Id: XM_038677445   ⟹   XP_038533373
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0943,400,250 - 43,406,983 (-)NCBI
RefSeq Acc Id: XM_038677447   ⟹   XP_038533375
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0943,400,250 - 43,406,982 (-)NCBI
RefSeq Acc Id: XM_038677448   ⟹   XP_038533376
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0943,400,250 - 43,406,984 (-)NCBI
RefSeq Acc Id: XM_537740   ⟹   XP_537740
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1942,581,117 - 42,587,830 (-)NCBI
Dog10K_Boxer_Tasha941,738,040 - 41,744,761 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_003435353   ⟸   XM_003435305
- UniProtKB: E2QWN9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_537740   ⟸   XM_537740
- UniProtKB: E2QWN9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000027528   ⟸   ENSCAFT00000029619
RefSeq Acc Id: ENSCAFP00000060249   ⟸   ENSCAFT00000071964
RefSeq Acc Id: XP_038342315   ⟸   XM_038486387
RefSeq Acc Id: XP_038342313   ⟸   XM_038486385
RefSeq Acc Id: XP_038342314   ⟸   XM_038486386
RefSeq Acc Id: XP_038468118   ⟸   XM_038612190
RefSeq Acc Id: XP_038468116   ⟸   XM_038612188
RefSeq Acc Id: XP_038468117   ⟸   XM_038612189
RefSeq Acc Id: XP_038533376   ⟸   XM_038677448
RefSeq Acc Id: XP_038533373   ⟸   XM_038677445
RefSeq Acc Id: XP_038533375   ⟸   XM_038677447
RefSeq Acc Id: XP_038466418   ⟸   XM_038610490
RefSeq Acc Id: XP_038404153   ⟸   XM_038548225
RefSeq Acc Id: XP_038404151   ⟸   XM_038548223
RefSeq Acc Id: XP_038404152   ⟸   XM_038548224
RefSeq Acc Id: ENSCAFP00845021499   ⟸   ENSCAFT00845027318
RefSeq Acc Id: ENSCAFP00845021485   ⟸   ENSCAFT00845027301

Promoters
RGD ID:13684669
Promoter ID:EPDNEW_C2737
Type:initiation region
Name:IFT20_1
Description:intraflagellar transport 20
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
CanFam3.1942,587,791 - 42,587,851EPDNEW
Damaging Variants


Assembly: CanFam3.1

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 42581494 42581495 A T snv Chinese indigenous dogs (DQ4)
9 42583941 42583942 G A snv Mixed Breed (MI016)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000018659 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030013952 UniProtKB/TrEMBL
  ENSCAFG00040019992 UniProtKB/TrEMBL
  ENSCAFG00845015286 Ensembl, ENTREZGENE
Ensembl Protein ENSCAFP00000027528 UniProtKB/TrEMBL
  ENSCAFP00000060249 UniProtKB/TrEMBL
  ENSCAFP00030022676 UniProtKB/TrEMBL
  ENSCAFP00030022732 UniProtKB/TrEMBL
  ENSCAFP00040032291 UniProtKB/TrEMBL
  ENSCAFP00040032309 UniProtKB/TrEMBL
  ENSCAFP00845021485 ENTREZGENE
Ensembl Transcript ENSCAFT00000029619 UniProtKB/TrEMBL
  ENSCAFT00000071964 UniProtKB/TrEMBL
  ENSCAFT00030025966 UniProtKB/TrEMBL
  ENSCAFT00030026031 UniProtKB/TrEMBL
  ENSCAFT00040037070 UniProtKB/TrEMBL
  ENSCAFT00040037090 UniProtKB/TrEMBL
  ENSCAFT00845027301 ENTREZGENE
InterPro FT20 UniProtKB/TrEMBL
KEGG Report cfa:480620 UniProtKB/TrEMBL
NCBI Gene IFT20 ENTREZGENE
PANTHER PTHR31978 UniProtKB/TrEMBL
Pfam IFT20 UniProtKB/TrEMBL
UniProt A0A5F4D0T1_CANLF UniProtKB/TrEMBL
  A0A8C0N7T2_CANLF UniProtKB/TrEMBL
  A0A8C0NC67_CANLF UniProtKB/TrEMBL
  E2QWN9 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:54957 ENTREZGENE