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TTLL3 Gene

protein-coding   GIFtS: 43
GCID: GC03P009851

Tubulin Tyrosine Ligase-Like Family, Member 3

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Tubulin Tyrosine Ligase-Like Family, Member 31 2
Tubulin--Tyrosine Ligase-Like Protein 32 3
HOTTL2 3
Tubulin Monoglycylase TTLL32
EC 6.3.2.-3

External Ids:    HGNC: 244831   Entrez Gene: 261402   Ensembl: ENSG000002140217   UniProtKB: Q9Y4R73   

Export aliases for TTLL3 gene to outside databases

Previous GC identifers: GC03P009836 GC03P009810 GC03P009811 GC03P009749 GC03P009813 GC03P009850 GC03P009788


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TTLL3 Gene:
TTLL3 (tubulin tyrosine ligase-like family, member 3) is a protein-coding gene. GO annotations related to this gene include protein-glycine ligase activity, initiating and protein-glycine ligase activity. An important paralog of this gene is TTLL4.

UniProtKB/Swiss-Prot: TTLL3_HUMAN, Q9Y4R7
Function: Monoglycylase which modifies alpha- and beta-tubulin, generating side chains of glycine on the
gamma-carboxyl groups of specific glutamate residues within the C-terminal tail of alpha- and beta-tubulin.
Involved in the side-chain initiation step of the glycylation reaction by adding a single glycine chain to
generate monoglycine side chains. Not involved in elongation step of the polyglycylation reaction

Gene Wiki entry for TTLL3 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the TTLL3 gene promoter:
         NF-1   p300   HEN1   AREB6   E2F-1   E2F   COMP1   SEF-1 (1)   TGIF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTTLL3 promoter sequence
   Search Chromatin IP Primers for TTLL3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TTLL3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3p25.3   Ensembl cytogenetic band:  3p25.3   HGNC cytogenetic band: 3p25.3

TTLL3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TTLL3 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P009851:  view genomic region     (about GC identifiers)

Start:
9,849,770 bp from pter      End:
9,896,822 bp from pter
Size:
47,053 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TTLL3_HUMAN, Q9Y4R7 (See protein sequence)
Recommended Name: Tubulin monoglycylase TTLL3  
Size: 772 amino acids; 87414 Da
Secondary accessions: Q4KMS8 Q6AWA3 Q6ZU95 Q8NDN8 Q96GG8 Q9H876 Q9UI99
Alternative splicing: 4 isoforms:  Q9Y4R7-1   Q9Y4R7-2   Q9Y4R7-5   Q9Y4R7-6   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TTLL3: NX_Q9Y4R7

Explore proteomics data for TTLL3 at MOPED


See TTLL3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001021100.3  
ENSEMBL proteins: 
 ENSP00000399930   ENSP00000399782   ENSP00000401686   ENSP00000414965   ENSP00000408128  
 ENSP00000394481   ENSP00000400462   ENSP00000402197   ENSP00000395912   ENSP00000392549  
 ENSP00000389904   ENSP00000398996   ENSP00000412915   ENSP00000396606   ENSP00000312148  
 ENSP00000473440   ENSP00000473376   ENSP00000399191   ENSP00000398097   ENSP00000373338  
 ENSP00000430051   ENSP00000409632   ENSP00000409246   ENSP00000403874   ENSP00000473314  
 ENSP00000446659   ENSP00000380416   ENSP00000394462  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
TTLL: Tubulin tyrosine ligase-like family

2 InterPro protein domains:
 IPR004344 TTL/TTLL_fam
 IPR027753 TTLL3/TTLL8

Graphical View of Domain Structure for InterPro Entry Q9Y4R7

ProtoNet protein and cluster: Q9Y4R7

1 Blocks protein domain: IPB004344 Tubulin-tyrosine ligase

UniProtKB/Swiss-Prot: TTLL3_HUMAN, Q9Y4R7
Similarity: Contains 1 TTL domain


Find genes that share domains with TTLL3           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: TTLL3_HUMAN, Q9Y4R7
Function: Monoglycylase which modifies alpha- and beta-tubulin, generating side chains of glycine on the
gamma-carboxyl groups of specific glutamate residues within the C-terminal tail of alpha- and beta-tubulin.
Involved in the side-chain initiation step of the glycylation reaction by adding a single glycine chain to
generate monoglycine side chains. Not involved in elongation step of the polyglycylation reaction

     Enzyme Number (IUBMB): EC 6.3.2.-1

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0070735protein-glycine ligase activity IDA19524510
GO:0070736protein-glycine ligase activity, initiating ISS--
     
Find genes that share ontologies with TTLL3           About GenesLikeMe


Animal Models:
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miRNA
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miRTarBase miRNAs that target TTLL3:
hsa-mir-124-3p (MIRT022524)

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3 qRT-PCR Assays for microRNAs that regulate TTLL3:
hsa-miR-3607-3p hsa-miR-3154 hsa-miR-513a-5p
SwitchGear 3'UTR luciferase reporter plasmidTTLL3 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat TTLL3

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
TTLL3_HUMAN, Q9Y4R7: Cytoplasm, cytoskeleton (By similarity). Cell projection, cilium (By similarity). Cytoplasm,
cytoskeleton, cilium axoneme (By similarity)

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005874microtubule IEA--
GO:0005929cilium ISS--
GO:0005930axoneme ISS--
GO:0015630microtubule cytoskeleton ISS--

Find genes that share ontologies with TTLL3           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for TTLL3 About    
See pathways by source

SuperPathContained pathways About
1Fcgamma receptor (FCGR) dependent phagocytosis
Regulation of actin dynamics for phagocytic cup formation0.77
Fcgamma receptor (FCGR) dependent phagocytosis0.77



    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TTLL3
Interactions:

    Search GeneGlobe Interaction Network for TTLL3

3 Interacting proteins for TTLL3 (Q9Y4R72, 3) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
ARPC5LQ9BPX52, 3MINT-65307 I2D: score=1 
NELFCDQ8IXH72, 3MINT-64863 I2D: score=1 
RNF130Q86XS82, 3MINT-64838 I2D: score=1 
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Gene Ontology (GO): 5 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006464cellular protein modification process ----
GO:0006952defense response ----
GO:0018094protein polyglycylation IDA19524510
GO:0035082axoneme assembly ISS--
GO:0042384cilium assembly ISS--

Find genes that share ontologies with TTLL3           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for TTLL3



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for TTLL3 gene (2 alternative transcripts): 
NM_015644.3  NM_001025930.3  

Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 36):
ENST00000414814 ENST00000452597 ENST00000419081 ENST00000438596 ENST00000459758
ENST00000417065 ENST00000439814 ENST00000418745 ENST00000430718 ENST00000427220(uc003btf.4)
ENST00000426895 ENST00000426827 ENST00000431204 ENST00000422738 ENST00000430390
ENST00000483051(uc003bth.4 uc011atj.2) ENST00000310252 ENST00000496526(uc010hco.1)

miRNA
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3 qRT-PCR Assays for microRNAs that regulate TTLL3:
hsa-miR-3607-3p hsa-miR-3154 hsa-miR-513a-5p
SwitchGear 3'UTR luciferase reporter plasmidTTLL3 3' UTR sequence
Inhib. RNA
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Primer
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OriGene qPCR primer pairs and template standards for TTLL3
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Pre-validated RT2 qPCR Primer Assay in human, mouse, rat TTLL3
  QuantiTect SYBR Green Assays in human, mouse, rat TTLL3
  QuantiFast Probe-based Assays in human, mouse, rat TTLL3

Selected AceView cDNA sequences (see all 645):

BM553110 AW517150 CA488436 AI864496 CR609636 AF019888 BU557128 AF006087 
BM547583 AI884770 AA577831 BF433287 BX425210 CR610621 BX416837 BM927852 
BP338685 AA865878 CB852324 CR600023 CA495372 CR591140 BM808570 BM809150 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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TTLL3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GTGAAACCGT
TTLL3 Expression
About this image


TTLL3 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 5) fully expand
 
 Limb (Muscoskeletal System)
         Mesenchymal Condensate Cells Zeugopod
 
 Bone (Muscoskeletal System)
         Mesenchymal Condensate Cells Zeugopod
 
 Cartilage (Muscoskeletal System)
         Mesenchymal Condensate Cells Zeugopod
 
 Testis (Reproductive System)
 
 Prostate (Endocrine System)
TTLL3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TTLL3 Protein Expression
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TTLL3

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for TTLL3 gene from Selected species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ttll31 , 5 tubulin tyrosine ligase-like family, member 31, 5 81.51(n)1
76.02(a)1
  6 (52.76 cM)5
1011001  NM_133923.61  NP_598684.41 
 1133892605 
chicken
(Gallus gallus)
Aves --
Uncharacterized protein
33(a)
1 → many
12(11472504-11474022)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
54(a)
1 → many
2(191293942-191322780)
zebrafish
(Danio rerio)
Actinopterygii ttll36
tubulin tyrosine ligase-like family, member 3
40(a)
1 → many
6(40260172-40287060) ENSDARG00000053728
fruit fly
(Drosophila melanogaster)
Insecta TTLL3B6
TTLL3A6
Tubulin tyrosine ligase-like 3A
23(a)
23(a)
many ↔ many
many ↔ many
2L(6732866-6736149)
2L(6736449-6740176)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PBY16
Putative tubulin tyrosine ligase associated with P...
13(a)
1 → many
II(432036-434297) YBR094W


ENSEMBL Gene Tree for TTLL3 (if available)
TreeFam Gene Tree for TTLL3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TTLL3 gene
TTLL42  TTLL102  ENSG000002611472  TTLL12  TTLL52  TTLL112  TTLL92  TTLL72  
TTLL62  TTL2  TTLL82  TTLL22  TTLL132  ARPC4-TTLL32  
2 SIMAP similar genes for TTLL3 using alignment to 23 protein entries:     TTLL3_HUMAN (see all proteins):
ARPC4-TTLL3    TTLL8

Find genes that share paralogs with TTLL3           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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6 SNPs for TTLL3    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 3 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
VAR_0360554
A colorectal cancer sample4--see VAR_0360552 M I mis40--------
VAR_0360544
A colorectal cancer sample4--see VAR_0360542 G S mis40--------
rs38066691,2,4
----see VAR_0524102 mis40--------
rs22903051,2,4
----see VAR_0202072 mis40--------
rs22903021,2,4
----see VAR_0524112 mis40--------
rs10572781,2,4
----see VAR_0524122 mis40--------

HapMap Linkage Disequilibrium report for TTLL3 (9849770 - 9896822 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for TTLL3:    About this table    
Variant IDTypeSubtypePubMed ID
nsv237238CNV Loss16902084
nsv834615CNV Loss17160897
nsv819644CNV Gain19587683

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing TTLL3
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for TTLL3 gene, integrated from 10 sources (see all 12):
(articles sorted by number of sources associating them with TTLL3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Evolutionary divergence of enzymatic mechanisms for posttranslational polyglycylation. (PubMed id 19524510)1, 2 Rogowski K....Janke C. (Cell 2009)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. Characterization of the human tubulin tyrosine ligase-like 1 gene (TTLL1) mapping to 22q13.1. (PubMed id 11054573)1, 3 Trichet V.... De Sario A. (Gene 2000)
  4. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
  5. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
  6. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
  7. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
  8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  9. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. (PubMed id 15342556)1 Suzuki Y.... Sugano S. (Genome Res. 2004)
  10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 26140 HGNC: 24483 AceView: ARPC4andTTLL3 Ensembl:ENSG00000214021 euGenes: HUgn26140
ECgene: TTLL3 H-InvDB: TTLL3

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for TTLL3 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for TTLL3 gene:
Search GeneIP for patents involving TTLL3

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(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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