Ttll4 (tubulin tyrosine ligase like 4) - Rat Genome Database

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Gene: Ttll4 (tubulin tyrosine ligase like 4) Rattus norvegicus
Analyze
Symbol: Ttll4
Name: tubulin tyrosine ligase like 4
RGD ID: 1594742
Description: Predicted to enable tubulin binding activity and tubulin-glutamic acid ligase activity. Predicted to be involved in microtubule cytoskeleton organization. Predicted to act upstream of or within regulation of blastocyst development. Predicted to be located in 9+0 non-motile cilium and ciliary basal body. Predicted to be active in cilium. Orthologous to human TTLL4 (tubulin tyrosine ligase like 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC690512; similar to tubulin tyrosine ligase-like family, member 4; tubulin monoglutamylase TTLL4; tubulin polyglutamylase TTLL4; tubulin tyrosine ligase-like family, member 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8983,670,788 - 83,706,891 (+)NCBIGRCr8
mRatBN7.2976,221,659 - 76,258,219 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl976,221,796 - 76,251,301 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0981,925,363 - 81,961,882 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl981,940,630 - 81,954,686 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0981,687,817 - 81,724,261 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4974,011,065 - 74,025,699 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera973,794,152 - 73,830,671 (+)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17499049   PMID:20530212   PMID:21074048   PMID:26829768   PMID:29593216  


Genomics

Comparative Map Data
Ttll4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8983,670,788 - 83,706,891 (+)NCBIGRCr8
mRatBN7.2976,221,659 - 76,258,219 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl976,221,796 - 76,251,301 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0981,925,363 - 81,961,882 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl981,940,630 - 81,954,686 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0981,687,817 - 81,724,261 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4974,011,065 - 74,025,699 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera973,794,152 - 73,830,671 (+)NCBICelera
Cytogenetic Map9q33NCBI
TTLL4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382218,710,835 - 218,759,724 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2218,710,835 - 218,755,416 (+)EnsemblGRCh38hg38GRCh38
GRCh372219,575,558 - 219,620,139 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362219,283,887 - 219,327,652 (+)NCBINCBI36Build 36hg18NCBI36
Build 342219,401,147 - 219,444,913NCBI
Celera2213,343,326 - 213,387,891 (+)NCBICelera
Cytogenetic Map2q35NCBI
HuRef2211,428,803 - 211,473,377 (+)NCBIHuRef
CHM1_12219,582,524 - 219,627,056 (+)NCBICHM1_1
T2T-CHM13v2.02219,197,391 - 219,244,038 (+)NCBIT2T-CHM13v2.0
Ttll4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39174,700,804 - 74,740,991 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl174,700,904 - 74,742,889 (+)EnsemblGRCm39 Ensembl
GRCm38174,661,645 - 74,701,832 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl174,661,745 - 74,703,730 (+)EnsemblGRCm38mm10GRCm38
MGSCv37174,708,328 - 74,744,547 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36174,594,961 - 74,631,180 (+)NCBIMGSCv36mm8
Celera175,216,789 - 75,252,776 (+)NCBICelera
Cytogenetic Map1C4NCBI
cM Map138.54NCBI
Ttll4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495545314,679,945 - 14,720,025 (-)NCBIChiLan1.0ChiLan1.0
TTLL4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213121,339,077 - 121,388,881 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B121,356,017 - 121,403,846 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B105,968,840 - 106,016,034 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B224,563,626 - 224,610,511 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B224,563,691 - 224,610,431 (+)Ensemblpanpan1.1panPan2
TTLL4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13725,303,818 - 25,341,315 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3725,273,110 - 25,340,512 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3726,123,846 - 26,160,606 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03725,319,791 - 25,356,071 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3725,319,910 - 25,356,002 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13725,224,607 - 25,260,995 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03725,158,861 - 25,195,634 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03725,179,670 - 25,216,226 (+)NCBIUU_Cfam_GSD_1.0
Ttll4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303174,810,537 - 174,859,089 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365691,153,447 - 1,194,269 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365691,153,376 - 1,201,704 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TTLL4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15120,773,185 - 120,793,194 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115120,748,537 - 120,791,825 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215133,817,235 - 133,820,673 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TTLL4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110104,612,946 - 104,656,926 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10104,613,026 - 104,656,622 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604094,745,779 - 94,790,597 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ttll4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248236,310,738 - 6,352,333 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248236,314,177 - 6,352,236 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ttll4
103 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:54
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000023067
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)93696235977814038Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94249534379271511Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95584784177026453Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95662771378595166Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)95662771378595166Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95662771378595166Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat


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 renal system reproductive system respiratory system appendage
High
Medium 1 20 40 24 19 24 1 1 63 24 41 11 1
Low 2 23 17 17 17 7 10 11 11 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023067   ⟹   ENSRNOP00000023067
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl976,221,796 - 76,251,301 (+)Ensembl
Rnor_6.0 Ensembl981,940,630 - 81,954,686 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105220   ⟹   ENSRNOP00000093298
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl976,221,796 - 76,251,301 (+)Ensembl
RefSeq Acc Id: NM_001427082   ⟹   NP_001414011
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8983,670,788 - 83,706,891 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414011 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000023067.5
  ENSRNOP00000093298.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000023067   ⟸   ENSRNOT00000023067
RefSeq Acc Id: ENSRNOP00000093298   ⟸   ENSRNOT00000105220
RefSeq Acc Id: NP_001414011   ⟸   NM_001427082
- UniProtKB: D4A331 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A331-F1-model_v2 AlphaFold D4A331 1-1193 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1594742 AgrOrtholog
BioCyc Gene G2FUF-27120 BioCyc
Ensembl Genes ENSRNOG00000017129 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023067.5 UniProtKB/TrEMBL
  ENSRNOT00000105220.1 UniProtKB/TrEMBL
Gene3D-CATH ATP-grasp fold, B domain UniProtKB/TrEMBL
InterPro Tub_tyr_ligase UniProtKB/TrEMBL
KEGG Report rno:690512 UniProtKB/TrEMBL
NCBI Gene 690512 ENTREZGENE
PANTHER TUBULIN POLYGLUTAMYLASE UniProtKB/TrEMBL
  TUBULIN POLYGLUTAMYLASE TTLL4 UniProtKB/TrEMBL
Pfam TTL UniProtKB/TrEMBL
PhenoGen Ttll4 PhenoGen
PROSITE TTL UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017129 RatGTEx
Superfamily-SCOP Glutathione synthetase ATP-binding domain-like UniProtKB/TrEMBL
UniProt A0A8I6AJT5_RAT UniProtKB/TrEMBL
  D4A331 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Ttll4  tubulin tyrosine ligase like 4  Ttll4  tubulin tyrosine ligase-like family, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Ttll4  tubulin tyrosine ligase-like family, member 4  LOC690512  similar to tubulin tyrosine ligase-like family, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC690512  similar to tubulin tyrosine ligase-like family, member 4  LOC681499  similar to tubulin tyrosine ligase-like family, member 4  Data merged from RGD:1595337 1643240 APPROVED
2006-11-20 LOC690512  similar to tubulin tyrosine ligase-like family, member 4      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC681499  similar to tubulin tyrosine ligase-like family, member 4      Symbol and Name status set to provisional 70820 PROVISIONAL