Homo sapiens gene TUBA4B, encoding tubulin, alpha 4b (pseudogene).
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 4 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at low level, only 9.2% of the average gene in this release. The sequence of this gene is defined by 11 GenBank accessions, some from lung (seen 3 times), brain, pineal gland (once), normal nasopharynx (once), pineal gland (once).
Alternative mRNA variants and regulation: The gene contains 8 distinct gt-ag introns. Transcription produces 5 different mRNAs, 4 alternatively spliced variants and 1 unspliced form. There are 2 probable alternative promotors (see the diagram). The mRNAs appear to differ by overlapping exons with different boundaries. 176 bp of this gene are antisense to spliced gene TUBA4A, raising the possibility of regulated alternate expression.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant aAug10).
Function: There are 5 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in a pathway (Downregulated of MTA-3 in ER-negative Breast Tumors) and processes (microtubule-based movement, protein polymerization). Proteins are expected to have molecular functions (GTP binding, nucleotide binding, structural molecule activity) and to localize in various compartments (nucleus, microtubule).
Protein coding potential: 4 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (4 complete), some containing domains Tubulin/FtsZ family, GTPase domain, Tubulin C-terminal domain [Pfam]. The remaining mRNA variant (unspliced) appears not to encode a good protein.
Isoform TUBA4B.bAug10 is annotated using as Met a Kozak-compatible a..AGG. start, thereby gaining 82 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by phosphorylation; ubiquitination, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 2, links to other databases and other names
Map: This gene TUBA4B maps on chromosome 2, at 2q35 according to Entrez Gene. In AceView, it covers 18.95 kb, from 220117966 to 220136917 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 80086, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as TUBA4B, TUBA4 or FLJ13940, LOC80086. It has been described as putative tubulin-like protein alpha-4B.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Tuba3a (e=2 10-90), EG626534 (e=10-89), Tuba1c (e=4 10-87), Tuba1aandTuba1b (e=4 10-87), LOC100042266 (e=5 10-86), Tuba3b (e=2 10-85), Tuba4a (e=4 10-85), EG434428 (e=8 10-85), Tuba8 (e=4 10-84), LOC636070 (e=6 10-84).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes mec-12 (e=5 10-84), 1N556 (e=10-83), tba-4 (e=2 10-81), tba-1 (e=2 10-81), tba-9 (e=3 10-81), tba-7 (e=10-77), tba-6 (e=4 10-76), tba-8 (e=6 10-75), tba-5 (e=3 10-74), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes TUA5 (e=5 10-78), TUA3 (e=5 10-78), TUA6 (e=9 10-77), TUA2 (e=2 10-76), TUA4 (e=2 10-76), TUA1 (e=4 10-74), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
TUBA4B Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 1.18 1.66 0.96 1.55 0.55 0.83 1.35 0.51 7.13 0.68 4.10 5.40 1.18 1.10 0.24 5.04 1.02 0.96 1.78 2.19 1.55 0.63 0.12 0.18 0.36 0.48 0.24 0.09 0.18 0.22 0.18 0.21 0.19 0.17 0.15 0.22 1.02 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene TUBA4B 5' 3' encoded on plus strand of chromosome 2 from 220,117,966 to 220,136,917 3 4 22 a 5 21 91 b 12 22 c 5 10 91 d e-u 1kb 0 176 bp exon 176 bp exon 300 bp uORF 176 bp exon 13101 bp [gt-ag] intron 3 GenBank accessions 46 bp exon 300 bp uORF 3635 bp [gt-ag] intron 3 GenBank accessions 1 RNA-seq supporting reads 1 Blood 134 bp exon 300 bp uORF 830 bp [gt-ag] intron 5 GenBank accessions 17 RNA-seq supporting reads 2 UHR pooled cells 10 Brain 5 Neuroblastoma (also 9 Primates bodymap) 300 bp uORF 1023 bp exon 1023 bp exon 4 accessions, some from brain pineal gland (seen once) capped 5' end, 1 accession Validated 3' end, 1 accession 1023 bp exon 176 bp exon 12803 bp [gt-ag] intron 2 GenBank accessions 3 RNA-seq supporting reads 1 UHR pooled cells 2 Neuroblastoma 344 bp exon 344 bp exon 3662 bp [gt-ag] intron 2 GenBank accessions 19 RNA-seq supporting reads 6 UHR pooled cells 9 Brain 4 Neuroblastoma (also 8 Primates bodymap) 107 bp exon 1173 bp [gt-ag] intron 3 GenBank accessions 88 RNA-seq supporting reads 27 UHR pooled cells 37 Brain 1 Blood 21 Neuroblastoma 2 Other (also 4 Primates bodymap) 503 bp exon 2 accessions, some from normal nasopharynx (seen once) 503 bp exon 117 bp exon 117 bp exon 3620 bp [gt-ag] intron 2 GenBank accessions 10 RNA-seq supporting reads 2 UHR pooled cells 6 Brain 2 Neuroblastoma (also 1 Primates bodymap) 149 bp exon 830 bp [gt-ag] intron 5 GenBank accessions 17 RNA-seq supporting reads 2 UHR pooled cells 10 Brain 5 Neuroblastoma (also 9 Primates bodymap) 1030 bp exon 3 accessions, some from lung (seen 2 times) pineal gland (once) 1030 bp exon 176 bp exon 12803 bp [gt-ag] intron 2 GenBank accessions 3 RNA-seq supporting reads 1 UHR pooled cells 2 Neuroblastoma 344 bp exon 344 bp exon 3667 bp [gt-ag] intron 1 GenBank accession 9 RNA-seq supporting reads 6 Brain 3 Neuroblastoma (also 3 Primates bodymap) 102 bp exon 1173 bp [gt-ag] intron 3 GenBank accessions 88 RNA-seq supporting reads 27 UHR pooled cells 37 Brain 1 Blood 21 Neuroblastoma 2 Other (also 4 Primates bodymap) 503 bp exon 1 accession 503 bp exon 653 bp exon 653 bp exon 1 accession from lung 653 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 1379 bp 241 aa 164 bp 489 bp 297 bp 2kb including Promoter 18945 bp 1kb
bAug10 1130 bp 84 aa 411 bp 464 bp 2kb probably including promoter 18768 bp 1kb
cAug10 1296 bp 78 aa 114 bp 945 bp 2kb possibly including promoter 5746 bp 1kb
dAug10 1125 bp 47 aa 517 bp 464 bp 2kb probably including promoter 18768 bp 1kb
eAug10-unspliced 653 bp 51 aa 222 bp 275 bp 2kb probably including promoter 653 bp 1kb

Gene neighbors and Navigator on chromosome 2q35 back to top
D C R P WNT6 C I P WNT10A D C R P C R CDK5R2 C I P G R R FAM134A C I R P ZFAND2B D C I R P ANKZF1 C I R P STK16 C I R P TUBA4B C R P DNAJB2 C I R P R R DES D C I R P SPEG C R P GMPPA C I R P ACCN4 C R P TMEM198 C R INHA D C I R P STK11IP C I R P SLC4A3 D C I R P R D C I R P PRKAG3 R D C R P FEV D C I R P CRYBA2 C R CCDC108 D C I R P IHH D C I R P SLC23A3andNHEJ1 C R P C2orf24 R D C I R P ATG9AandABCB6 C R P GLB1L D C I R P TUBA4A D C I R P PTPRN C R P RESP18 R C I R P DNPEP R C I R P CHPF D C R P OBSL1 G P 100kb 0 CYP27A1, 427 accessions 12 variants WNT6, 27 accessions, 2 variants WNT10A, 71 accessions 3 variants teystuby, 1 accession slaklu, 6 accessions CDK5R2, 53 accessions LOC151300, 33 accessions 2 variants kakore, 7 accessions, 2 variants FAM134A, 497 accessions 12 variants ZFAND2B, 232 accessions 22 variants ANKZF1, 409 accessions 31 variants STK16, 335 accessions 16 variants TUBA4B, 11 accessions 5 variants DNAJB2, 443 accessions 21 variants toystuby, 1 accession kargabo, 10 accessions 2 variants DES, 419 accessions, 8 variants SPEG, 211 accessions, 28 variants GMPPA, 393 accessions 24 variants ACCN4, 59 accessions, 8 variants TMEM198, 108 accessions 7 variants INHA, 86 accessions, 4 variants STK11IP, 201 accessions 17 variants SLC4A3, 167 accessions 13 variants namemo, 7 accessions, 2 variants dergoybo, 2 accessions spawgarbu, 2 accessions spergarbu, 1 accession dorgoybo, 2 accessions sporgarbu, 1 accession spoygarbu, 1 accession fagoybo, 1 accession smoypabo, 1 accession luswuby, 1 accession leeswuby, 1 accession soheyo, 1 accession nadee, 2 accessions sokore, 6 accessions stugarbu, 1 accession stogarbu, 1 accession fogoybo, 1 accession steygarbu, 3 accessions storgarbu, 1 accession fawgoybo, 1 accession stoygarbu, 1 accession chormawbo, 1 accession nodee, 5 accessions swagarbu, 1 accession sharmawbo, 1 accession manimo, 2 accessions, 2 variants minimo, 2 accessions, 2 variants wylu, 1 accession swogarbu, 1 accession swargarbu, 2 accessions swergarbu, 1 accession feygoybo, 1 accession sweygarbu, 1 accession loyswuby, 9 accessions 2 variants swoygarbu, 1 accession bugawbu, 1 accession bargawbu, 1 accession bawgawbu, 1 accession beegawbu, 1 accession borgawbu, 3 accessions kuheyo, 3 accessions flermawbo, 1 accession myswuby, 1 accession fleymawbo, 1 accession keheyo, 3 accessions gargoybo, 2 accessions dergawbu, 1 accession deygawbu, 1 accession narswuby, 1 accession klermawbo, 1 accession goygoybo, 3 accessions fogawbu, 2 accessions radee, 12 accessions forgawbu, 1 accession foygawbu, 1 accession gagawbu, 2 accessions gygawbu, 1 accession puswuby, 1 accession menimo, 1 accession sune, 5 accessions gargawbu, 3 accessions smoklu, 1 accession sporpabo, 1 accession jugawbu, 1 accession jawgawbu, 2 accessions pleemawbo, 1 accession jeegawbu, 1 accession rene, 2 accessions deygoybo, 1 accession wyveybo, 1 accession stagarbu, 1 accession fugoybo, 1 accession lerswuby, 50 accessions stargarbu, 1 accession stawgarbu, 2 accessions kaheyo, 7 accessions stergarbu, 1 accession walu, 4 accessions snopabo, 3 accessions leyswuby, 1 accession hemayo, 11 accessions 2 variants swygarbu, 1 accession slyklu, 2 accessions swugarbu, 2 accessions sneepabo, 2 accessions pydee, 4 accessions swawgarbu, 1 accession flumawbo, 1 accession sluklu, 5 accessions sloklu, 2 accessions sweegarbu, 3 accessions kiheyo, 2 accessions wulu, 9 accessions sterkoy, 10 accessions podee, 1 accession slarklu, 3 accessions bagawbu, 1 accession forgoybo, 1 accession woveybo, 2 accessions bygawbu, 1 accession bogawbu, 2 accessions slawklu, 1 accession flarmawbo, 1 accession bergawbu, 1 accession fleemawbo, 6 accessions beygawbu, 2 accessions gygoybo, 1 accession gogoybo, 1 accession merswuby, 1 accession meyswuby, 1 accession glomawbo, 1 accession moyswuby, 1 accession dargawbu, 1 accession gawgoybo, 1 accession munimo, 2 accessions, 2 variants gergoybo, 2 accessions geygoybo, 1 accession glormawbo, 1 accession doygawbu, 3 accessions wawveybo, 1 accession fugawbu, 1 accession weeveybo, 2 accessions fawgawbu, 1 accession smaklu, 1 accession feegawbu, 1 accession fergawbu, 1 accession kikore, 3 accessions klormawbo, 1 accession rudee, 9 accessions, 2 variants nerswuby, 9 accessions plamawbo, 1 accession norswuby, 3 accessions gugawbu, 1 accession rardee, 4 accessions geegawbu, 2 accessions reedee, 1 accession gergawbu, 2 accessions jargoybo, 1 accession PRKAG3, 23 accessions 3 variants nydee, 6 accessions, 2 variants FEV, 23 accessions, 3 variants CRYBA2, 119 accessions 7 variants CCDC108, 79 accessions 15 variants IHH, 53 accessions SLC23A3andNHEJ1, 220 accessions 25 variants C2orf24, 415 accessions 9 variants lerkerbo, 1 accession ATG9AandABCB6, 716 accessions 27 variants GLB1L, 173 accessions 10 variants TUBA4A, 341 accessions 14 variants PTPRN, 442 accessions 21 variants RESP18, 9 accessions, 3 variants gleywawbo, 6 accessions 2 variants DNPEP, 483 accessions 24 variants poydee, 1 accession CHPF, 277 accessions, 3 variants OBSL1, 437 accessions 29 variants LOC100129746, 1 accession ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               5 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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