Homo sapiens gene ZNF154, encoding zinc finger protein 154.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
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 5 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.8 times the average gene in this release. The sequence of this gene is defined by 87 GenBank accessions from 83 cDNA clones, some from brain (seen 6 times), germinal center B cell (5), head neck (5), breast (4), colon (4), clones donated by kazusa DNA research inst (3), testis (3) and 29 other tissues.
Alternative mRNA variants and regulation: The gene contains 6 distinct gt-ag introns. Transcription produces 7 different mRNAs, 5 alternatively spliced variants and 2 unspliced forms. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, splicing versus retention of 4 introns.
2 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
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, bAug10, cAug10).
Function: There is one article specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in a process (regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (transcription factor activity, metal ion binding, zinc ion binding) and to localize in various compartments (nucleus, intracellular).
Protein coding potential: 4 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 COOH complete), some containing domains KRAB box, Zinc finger, C2H2 type [Pfam]. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 2 partial) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 19, links to other databases and other names
Map: This gene ZNF154 maps on chromosome 19, at 19q13.4 according to Entrez Gene. In AceView, it covers 13.14 kb, from 58220579 to 58207437 (NCBI 37, August 2010), on the reverse strand.
Links to: the SNP view, gene overviews from Entrez Gene 7710, GeneCards, expression data from ECgene, UniGene Hs.646378, Hs.649031, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as ZNF154, pHZ-92, MGC176628, MGC176661 or LOC7710, toreri. It has been described as zinc finger protein 154.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Zfp46 (e= 10-115), D10627 (e= 10-113), Zfp551 (e= 10-112), Zfp708 (e= 10-112), Zfp160 (e= 10-109), Zfp712 (e= 10-108), Zfp647 (e= 10-108), Zfp189 (e= 10-107), Zik1 (e= 10-107), Zfp418 (e= 10-107), Zfp2 (e= 10-107), Zfp113 (e= 10-106), Zfp184 (e= 10-105), Zfp629 (e= 10-105), Zfp273 (e= 10-105), Zfp420 (e= 10-105), RP23-442I10.2 (e= 10-105).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 4B812 (e=2 10-46).
The closest A.thaliana genes, according to BlastP, are the AceView genes ELF6 (e=9 10-10), REF6 (e=10-09), AT4G06634 (e=3 10-09), AT1G72050 (e=8 10-08)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
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!.
Read more...
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
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.
Read more...
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 2746 bp 437 aa 240 bp 1192 bp 90 bp 2kb probably including promoter 8769 bp 1kb
bAug10 2568 bp 437 aa 224 bp 1030 bp 90 bp 2kb including Promoter 11829 bp 1kb
cAug10 6983 bp 437 aa 197 bp 5472 bp 90 bp 2kb probably including promoter 13098 bp 1kb
dAug10 829 bp 68 aa 620 bp 2kb 2268 bp 1kb
eAug10-unspliced 2737 bp 93 aa 536 bp 1919 bp 2kb 2737 bp 1kb
fAug10-unspliced 621 bp 90 aa 350 bp 2kb 621 bp 1kb
gAug10 303 bp 34 aa 199 bp 2kb 3647 bp 1kb

Gene neighbors and Navigator on chromosome 19q13.4 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               1 article in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e-u, .f-u, .g 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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !