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TTLL9 Gene

protein-coding   GIFtS: 40
GCID: GC20P030458

Tubulin Tyrosine Ligase-Like Family, Member 9

(Previous name: chromosome 20 open reading frame 125)
(Previous symbol: C20orf125)
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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 91 2     dJ310O13.12
C20orf1251 2 3     Probable Tubulin Polyglutamylase TTLL92
Tubulin--Tyrosine Ligase-Like Protein 92 3     EC 6.-.-.-3
Chromosome 20 Open Reading Frame 1251     

External Ids:    HGNC: 161181   Entrez Gene: 1643952   Ensembl: ENSG000001310447   UniProtKB: Q3SXZ73   

Export aliases for TTLL9 gene to outside databases

Previous GC identifers: GC20P029925 GC20P027247


(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 TTLL9 Gene:
TTLL9 (tubulin tyrosine ligase-like family, member 9) is a protein-coding gene. GO annotations related to this gene include ligase activity. An important paralog of this gene is TTLL4.

UniProtKB/Swiss-Prot: TTLL9_HUMAN, Q3SXZ7
Function: Probable tubulin polyglutamylase that forms polyglutamate side chains on tubulin. Probably acts when
complexed with other proteins (By similarity)




(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 TTLL9 gene promoter:
         AhR   Spz1   Nkx2-5   AP-2gamma   POU3F2   GATA-2   AREB6   AP-2beta   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTTLL9 promoter sequence
   Search Chromatin IP Primers for TTLL9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TTLL9


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

Entrez Gene cytogenetic band: 20q11.21   Ensembl cytogenetic band:  20q11.21   HGNC cytogenetic band: 20q11

TTLL9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TTLL9 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P030458:  view genomic region     (about GC identifiers)

Start:
30,458,505 bp from pter      End:
30,532,764 bp from pter
Size:
74,260 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TTLL9_HUMAN, Q3SXZ7 (See protein sequence)
Recommended Name: Probable tubulin polyglutamylase TTLL9  
Size: 439 amino acids; 51472 Da
Sequence caution: Sequence=CAI42576.1; Type=Erroneous gene model prediction; Sequence=CAI42577.1; Type=Erroneous
gene model prediction; Sequence=EAW76401.1; Type=Erroneous gene model prediction;
Secondary accessions: A6NH06 A6NIS5 B3KSG8 Q3SXZ8 Q5JYS3 Q5JYS4
Alternative splicing: 3 isoforms:  Q3SXZ7-1   Q3SXZ7-2   Q3SXZ7-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TTLL9: NX_Q3SXZ7

Explore proteomics data for TTLL9 at MOPED


See TTLL9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001008409.1  
ENSEMBL proteins: 
 ENSP00000365105   ENSP00000442515   ENSP00000365100   ENSP00000365088   ENSP00000308980  
 ENSP00000365086  

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Cloud-Clone Corp. Proteins for TTLL9

 
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antibodies-online proteins for TTLL9 (4 products) 

 
Search antibodies-online for peptides for TTLL9

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antibodies-online kits for TTLL9 (8 products) 


(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:
 IPR027751 TTLL9
 IPR004344 TTL/TTLL_fam

Graphical View of Domain Structure for InterPro Entry Q3SXZ7

ProtoNet protein and cluster: Q3SXZ7

1 Blocks protein domain: IPB004344 Tubulin-tyrosine ligase

UniProtKB/Swiss-Prot: TTLL9_HUMAN, Q3SXZ7
Similarity: Contains 1 TTL domain


Find genes that share domains with TTLL9           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: TTLL9_HUMAN, Q3SXZ7
Function: Probable tubulin polyglutamylase that forms polyglutamate side chains on tubulin. Probably acts when
complexed with other proteins (By similarity)

     Enzyme Number (IUBMB): EC 6.-.-.-1

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016874ligase activity IEA--
     
Find genes that share ontologies with TTLL9           About GenesLikeMe


Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for TTLL9

miRNA
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Search for qRT-PCR Assays for microRNAs that regulate TTLL9
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Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat TTLL9

Gene Editing
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OriGene ORF clones in mouse, rat for TTLL9
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GenScript: all cDNA clones in your preferred vector: TTLL9 (NM_001008409)
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DNA2.0 Custom Codon Optimized Gene Synthesis Service for TTLL9
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TTLL9

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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
TTLL9_HUMAN, Q3SXZ7: Cytoplasm, cytoskeleton, cilium basal body (By similarity). Cytoplasm, cytoskeleton (By
similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytoskeleton3
cytosol2
nucleus2
endoplasmic reticulum1
mitochondrion1

Gene Ontology (GO): 3 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm IEA--
GO:0005874microtubule IEA--
GO:0005929cilium IEA--

Find genes that share ontologies with TTLL9           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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TTLL9
Interactions:

    Search GeneGlobe Interaction Network for TTLL9

STRING Interaction Network Preview (showing 5 interactants - click image to see 20)

Selected Interacting proteins for TTLL9 (ENSP000003651054) via UniProtKB, MINT, STRING, and/or I2D (see all 20)
InteractantInteraction Details
GeneCardExternal ID(s)
DCP1BENSP000002806654STRING: ENSP00000280665
PRDX1ENSP000002627464STRING: ENSP00000262746
PRDX2ENSP000003015224STRING: ENSP00000301522
PRDX3ENSP000002985104STRING: ENSP00000298510
PRDX4ENSP000003686464STRING: ENSP00000368646
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Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006464cellular protein modification process IEA--

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(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
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for TTLL9



(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 TTLL9 gene: 
NM_001008409.2  

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000375938(uc002wxc.2 uc002wwy.1 uc002wxa.1 uc002wxb.1 uc010ztp.1)
ENST00000535842(uc010gdx.1) ENST00000375934(uc010ztq.1 uc010zto.1)
ENST00000375922 ENST00000310998 ENST00000375921(uc002wwz.1)
miRNA
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Inhib. RNA
Products:
     
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Predesigned siRNA for gene silencing in human, mouse, rat TTLL9
Clone
Products:
     
OriGene clones in human, mouse for TTLL9 (see all 6)
OriGene ORF clones in mouse, rat for TTLL9
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
GenScript: all cDNA clones in your preferred vector: TTLL9 (NM_001008409)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for TTLL9
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TTLL9
Primer
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OriGene qSTAR qPCR primer pairs in human, mouse for TTLL9
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat TTLL9
  QuantiTect SYBR Green Assays in human, mouse, rat TTLL9
  QuantiFast Probe-based Assays in human, mouse, rat TTLL9

Selected AceView cDNA sequences (see all 29):

AA648367 AA897604 AK090839 AI871204 AW104364 BC068593 BG211546 AL040619 
AK093491 BC036213 BI459841 BF346221 BX096895 BU679850 AL161969 AX748163 
CD243364 AI352198 AW341668 AI693758 BG185673 AA811957 BF918876 BG036699 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for TTLL9 (see all 6)    About this scheme

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b
SP1:                                      -                 -                       -                 -                           
SP2:                                      -           -                             -     -           -                           
SP3:                                      -           -     -                                         -                           
SP4:                          -           -                 -           -           -     -     -     -                           
SP5:                                      -           -     -     -     -           -                                             


ECgene alternative splicing isoforms for TTLL9

(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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TTLL9 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTCATAGGTT
TTLL9 Expression
About this image


TTLL9 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Eye (Sensory Organs)
         Retina
 
 Testis (Reproductive System)
TTLL9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TTLL9 Protein Expression
    Custom PCR Arrays for TTLL9
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TTLL9

(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 TTLL9 gene from Selected species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ttll91 , 5 tubulin tyrosine ligase-like family, member 91, 5 85.61(n)1
90.89(a)1
  2 (75.41 cM)5
747111  NM_001083618.11  NP_001077087.11 
 1529624855 
chicken
(Gallus gallus)
Aves TTLL91 tubulin tyrosine ligase-like family, member 9 71.89(n)
74.29(a)
  771843  XM_003642467.2  XP_003642515.2 
lizard
(Anolis carolinensis)
Reptilia TTLL96
tubulin tyrosine ligase-like family, member 9
75(a)
1 ↔ 1
GL343505.1(48884-81762)
zebrafish
(Danio rerio)
Actinopterygii ttll91 tubulin tyrosine ligase-like family, member 9 69.93(n)
72.55(a)
  556794  NM_001256764.1  NP_001243693.1 
worm
(Caenorhabditis elegans)
Secernentea ttll-91 ttll-9 53.73(n)
51.27(a)
  3564837  NM_001028670.1  NP_001023841.1 
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PBY16
Putative tubulin tyrosine ligase associated with P...
10(a)
1 → many
II(432036-434297) YBR094W


ENSEMBL Gene Tree for TTLL9 (if available)
TreeFam Gene Tree for TTLL9 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TTLL9 gene
TTLL42  TTLL102  ENSG000002611472  TTLL32  TTLL12  TTLL52  TTLL112  TTLL72  
TTLL62  TTL2  TTLL82  TTLL22  TTLL132  ARPC4-TTLL32  
3 SIMAP similar genes for TTLL9 using alignment to 3 protein entries:     TTLL9_HUMAN (see all proteins):
TTLL1    TTLL4    TTLL5

Find genes that share paralogs with TTLL9           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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Selected SNPs for TTLL9 (see all 1480)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2012856061,2
Cuntested130513893(+) AGACAG/AGGTAT 2 /Q syn11Minor allele frequency- A:0.00EU 1317
rs1445837881,2
--30460481(+) AGAGCA/GAGACC 1 -- int10--------
rs1866142671,2
--30460517(+) ACACAC/TGAAAA 1 -- int10--------
rs1913097401,2
C--30460534(+) AGAGTG/TGAGAG 1 -- int10--------
rs1144677771,2
F--30460586(+) GATGGG/AAATAG 1 -- int11Minor allele frequency- A:0.08WA 118
rs1480405451,2
C--30460602(+) CCTCTA/GTAAAA 1 -- int10--------
rs739036691,2
C,F--30460700(+) ATTGGG/CAGTTA 1 -- int13Minor allele frequency- C:0.11WA NA 240
rs622062851,2
C,F--30460793(+) AAATAC/TTTCGA 1 -- int13Minor allele frequency- T:0.02NA EU 691
rs60584751,2
C,F,A,H--30460869(+) tgggaT/Cagagt 1 -- int121Minor allele frequency- C:0.14NS EA NA WA CSA EU 2546
rs801565541,2
F--30460967(+) GATGTG/TGGGGG 1 -- int11Minor allele frequency- T:0.04EA 120

HapMap Linkage Disequilibrium report for TTLL9 (30458505 - 30532764 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for TTLL9:    About this table    
Variant IDTypeSubtypePubMed ID
nsv3347CNV Insertion18451855
nsv912836CNV Loss21882294
nsv833952CNV Gain17160897
nsv817890CNV Gain17921354
esv21897CNV Gain19812545
nsv517635CNV Gain19592680

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing TTLL9
DNA2.0 Custom Variant and Variant Library Synthesis for TTLL9

(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 TTLL9 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TTLL9)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Tubulin polyglutamylase enzymes are members of the TTL domain protein family. (PubMed id 15890843)1, 3 Janke C.... Edde B. (Science 2005)
  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. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  4. 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)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  6. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)2 Deloukas P....Rogers J. (Nature 2001)

(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: 164395 HGNC: 16118 AceView: LOC164395 Ensembl:ENSG00000131044 euGenes: HUgn164395
ECgene: TTLL9 H-InvDB: TTLL9

(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 TTLL9 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 TTLL9 gene:
Search GeneIP for patents involving TTLL9

GeneCards and IP:
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