Homo sapiens gene GLIS2, encoding GLIS family zinc finger 2.
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SUMMARY back to top
RefSeq summary
[GLIS2] This gene is a member of the GLI-similar zinc finger protein family and encodes a nuclear transcription factor with five C2H2-type zinc finger domains. The protein encoded by this gene is widely expressed at low levels in the neural tube and peripheral nervous system and likely promotes neuronal differentiation. It is abundantly expressed in the kidney and may have a role in the regulation of kidney morphogenesis. p120 regulates the expression level of this protein and induces the cleavage of this protein's C-terminal zinc finger domain. This protein also promotes the nuclear translocation of p120. Mutations in this gene cause nephronophthisis (NPHP), an autosomal recessive kidney disease characterized by tubular basement membrane disruption, interstitial lymphohistiocytic cell infiltration, and development of cysts at the corticomedullary border of the kidneys.

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 2 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 1.3 times the average gene in this release. The sequence of this gene is defined by 150 GenBank accessions from 129 cDNA clones, some from brain (seen 17 times), pancreas (12), eye (8), lung (8), kidney (7), uterus (7), small intestine (6) and 72 other tissues. We annotate structural defects or features in 9 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 7 distinct gt-ag introns. Transcription produces 3 different mRNAs, 2 alternatively spliced variants and 1 unspliced form. There are 2 non overlapping alternative last exons (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end.
Function: There are 7 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to a disease (OMIM: Nephronophthisis 7) and proposed to participate in processes (cell differentiation, multicellular organismal development, negative regulation of transcription, nervous system development, positive regulation of transcription). Proteins are expected to have molecular functions (DNA binding, metal ion binding, transcription activator activity, zinc ion binding) and to localize in various compartments (nucleus, cytoplasm, intracellular, nuclear speck). A putative protein interactor has been described (CTNNB1).
Protein coding potential: The 2 spliced and the unspliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 COOH complete), some containing Zinc finger, C2H2 type domain [Pfam]. Finally proteins from this gene may be modulated by phosphorylation, 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 16, links to other databases and other names
Map: This gene GLIS2 maps on chromosome 16, at 16p13.3 according to Entrez Gene. In AceView, it covers 25.28 kb, from 4364763 to 4390042 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from OMIM_611498, PhosphoSite, the SNP view, gene overviews from Entrez Gene 84662, 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 GLIS2, NKL, NPHP7, FLJ38247 or LOC84662, godyby. It has been described as zinc finger protein GLIS2, GLI-similar 2, nephrocystin-7, GLI-similar protein 2, neuronal Krueppel-like protein, Kruppel-like zinc finger protein GLIS2.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Glis2 (e=5 10-17).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes tra-1 (e=2 10-09), ref-2 (e=2 10-07), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes REF6 (e=0.099), ELF6 (e=0.33), AT5G22890 (e=0.49), 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
GLIS2 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 0.36 7.64 0.22 2.90 0.34 1.18 1.02 2.52 8.19 4.39 16.4 0.51 14.3 8.19 0.63 43.2 10.1 0.27 0.19 0.39 0.39 5.79 1.55 0.36 0.32 1.26 2.19 1.02 0.36 0.36 0.48 0.72 1.26 3.57 0.36 0.32 0.63 3.82 0.17 0.39 0.15 1.91 2.70 0.89 0.16 0.39 0.36 0.08 1.02 0.63 2.05 0.55 2.19 3.57 0.45 0.48 0.96 0.89 1.45 3.33 0.39 0.12 0.11 0.21 0.21 0.68 0.12 1.26 2.90 1.91 0.15 0.10 0.15 1.18 0.29 0.32 0.59 0.32 0.68 0.72 1.10 0.51 1.45 0.08 0.89 0.18 0.16 0.27 0.17 0.10 0.59 1.78 0.14 0.29 0.32 0.89 0.15 0.17 0.12 0.32 1.66 1.45 0.36 0.89 0.10 0.08 0.08 0.42 0.32 0.68 0.19 0.55 0.42 1.55 2.35 0.13 0.55 0.48 0.55 0.34 1.91 2.70 0.83 1.45 0.83 0.06 0.15 0.59 0.68 0.26 0.29 0.68 0.16 1.10 0.08 0.34 0.19 1.18 0.17 1.26 0.42 0.42 0.55 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 GLIS2 5' 3' encoded on plus strand of chromosome 16 from 4,364,763 to 4,390,042 8 94 24719 15364 29960 a [NM] 15364 b c-u 1 2kb 0 694 bp exon 13654 bp [gt-ag] intron 1 GenBank accession 7 RNA-seq supporting reads 2 Brain 4 Neuroblastoma 1 Other 60 bp exon 3045 bp [gt-ag] intron 1 GenBank accession 93 RNA-seq supporting reads 11 UHR pooled cells 13 Brain 1 Blood 66 Neuroblastoma 2 Other 238 bp exon 238 bp exon 894 bp [gt-ag] intron 6 GenBank accessions 24713 RNA-seq supporting reads 2486 UHR pooled cells 2434 Brain 38 Blood 19505 Neuroblastoma 250 Other (also 1090 Primates bodymap) 173 bp exon 1281 bp [gt-ag] intron 10 GenBank accessions 15354 RNA-seq supporting reads 1488 UHR pooled cells 1468 Brain 6 Blood 12250 Neuroblastoma 142 Other (also 347 Primates bodymap) 177 bp exon 82 bp [gt-ag] intron 9 GenBank accessions 21217 RNA-seq supporting reads 2350 UHR pooled cells 2252 Brain 12 Blood 16405 Neuroblastoma 198 Other (also 418 Primates bodymap) 134 bp exon 81 bp [gt-ag] intron 12 GenBank accessions 24889 RNA-seq supporting reads 2681 UHR pooled cells 2590 Brain 21 Blood 19360 Neuroblastoma 237 Other (also 661 Primates bodymap) 119 bp exon 1331 bp [gt-ag] intron 11 GenBank accessions 29949 RNA-seq supporting reads 3066 UHR pooled cells 3203 Brain 21 Blood 23418 Neuroblastoma 241 Other (also 558 Primates bodymap) 3317 bp exon 127 accessions, NM_032575.2 some from brain (seen 14 times) pancreas (9), lung (8) eye (7), kidney (7) capped 5' end, 16 accessions Validated 3' end, 33 accessions 3317 bp exon 367 bp exon 367 bp exon 1281 bp [gt-ag] intron 10 GenBank accessions 15354 RNA-seq supporting reads 1488 UHR pooled cells 1468 Brain 6 Blood 12250 Neuroblastoma 142 Other (also 347 Primates bodymap) 177 bp exon 82 bp [gt-ag] intron 9 GenBank accessions 21217 RNA-seq supporting reads 2350 UHR pooled cells 2252 Brain 12 Blood 16405 Neuroblastoma 198 Other (also 418 Primates bodymap) 155 bp exon 2 accessions, some from brain (seen once) lung normal (once) 155 bp exon 1053 bp exon 1053 bp exon 2 accessions, some from pancreas (seen once) purified pancreatic islet (once) 1053 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 Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aAug10 4912 bp 524 aa 820 bp 2517 bp 2kb including Promoter 25280 bp 1kb
bAug10 699 bp 226 aa 17 bp 2kb 2062 bp 1kb
cAug10-unspliced 1053 bp 120 aa 460 bp 230 bp 2kb possibly including promoter 1053 bp 1kb

Gene neighbors and Navigator on chromosome 16p13.3 back to top
GLIS2 D C I R P VASN C I R P DNAJA3 D C I R P C C HMOX2 D C I R P G C P MGRN1 C R P NUDT16L1 C R P C16orf71 C R G C R C R P ADCY9 C R P SRL C R C I R P TFAP4 C P C I R P CORO7andTIMM16 C R P NMRAL1 C R P C16orf5 C I R P FAM100A C I R P ZNF500andANKS3 C R P SEPT12 R C I R ROGDI 100kb 0 GLIS2, 140 accessions 3 variants VASN, 208 accessions, 2 variants DNAJA3, 547 accessions 11 variants steesnor, 1 accession hutoma, 1 accession HMOX2, 465 accessions 15 variants LOC342346, 11 accessions MGRN1, 340 accessions 21 variants NUDT16L1, 292 accessions 5 variants C16orf71, 119 accessions 6 variants LOC440335, 38 accessions 8 variants kladaby, 1 accession gloysnor, 1 accession klasnor, 1 accession klysnor, 2 accessions klosnor, 1 accession klarsnor, 1 accession zyza, 2 accessions hisuru, 7 accessions kleedaby, 1 accession zuza, 1 accession plysnor, 5 accessions pleedaby, 1 accession plosnor, 1 accession plarsnor, 1 accession zeenoy, 1 accession pleesnor, 1 accession plersnor, 1 accession smodaby, 1 accession ploysnor, 1 accession skasnor, 3 accessions skysnor, 1 accession skosnor, 1 accession skarsnor, 1 accession skawsnor, 1 accession skersnor, 2 accessions skorsnor, 3 accessions slasnor, 1 accession slysnor, 1 accession slusnor, 1 accession steyru, 3 accessions sleesnor, 2 accessions vorzobu, 2 accessions swardaby, 1 accession wazobu, 1 accession zeynoy, 1 accession smusnor, 1 accession smawsnor, 1 accession zoyglee, 1 accession smoysnor, 1 accession beedyby, 2 accessions snusnor, 2 accessions snarsnor, 1 accession snawsnor, 1 accession snersnor, 1 accession snoysnor, 1 accession swarru, 1 accession sposnor, 2 accessions chanoy, 1 accession chawnoy, 1 accession weezobu, 1 accession speysnor, 1 accession geydyby, 1 accession jodyby, 1 accession jardyby, 1 accession weyzobu, 1 accession saruru, 1 accession speeseybo, 1 accession storsnor, 4 accessions woyzobu, 1 accession swysnor, 3 accessions swosnor, 1 accession kawdyby, 1 accession swawsnor, 1 accession zuzobu, 1 accession moydyby, 2 accessions sweysnor, 1 accession buro, 2 accessions bysnoy, 1 accession nodyby, 1 accession barsnoy, 1 accession radyby, 1 accession ploysmer, 14 accessions shawglee, 3 accessions zerzobu, 5 accessions blunoy, 5 accessions roydyby, 1 accession sordyby, 1 accession zoyza, 2 accessions bleenoy, 1 accession dawsnoy, 1 accession zoyzobu, 1 accession sheyglee, 2 accessions wodyby, 1 accession deysnoy, 1 accession chyzobu, 3 accessions chuzobu, 4 accessions fasnoy, 3 accessions fysnoy, 1 accession sperseybo, 2 accessions zawdyby, 1 accession sherdyby, 1 accession skasmer, 1 accession charzobu, 1 accession fersnoy, 1 accession klawdyby, 1 accession gasnoy, 1 accession glunoy, 3 accessions gysnoy, 2 accessions gusnoy, 1 accession pleedyby, 1 accession flydaby, 1 accession gleesnor, 4 accessions zaza, 3 accessions glorsnor, 2 accessions klawsnor, 3 accessions torzobu, 2 accessions kleesnor, 1 accession klersnor, 1 accession klydaby, 1 accession skeydo, 4 accessions reyu, 2 accessions klorsnor, 2 accessions starru, 2 accessions kloysnor, 1 accession plusnor, 1 accession zoza, 8 accessions, 2 variants sleedaby, 1 accession vazobu, 1 accession zarza, 2 accessions steeru, 5 accessions, 2 variants plawsnor, 1 accession slado, 2 accessions zawnoy, 1 accession sloydaby, 1 accession vyzobu, 1 accession vuzobu, 1 accession pleysnor, 1 accession smoydaby, 1 accession snydaby, 1 accession skusnor, 1 accession skeesnor, 3 accessions skeysnor, 2 accessions zeyglee, 1 accession veezobu, 1 accession zorglee, 1 accession sneedaby, 1 accession verzobu, 1 accession sterru, 4 accessions sperdaby, 1 accession stoydaby, 1 accession slosnor, 1 accession slarsnor, 2 accessions slawsnor, 2 accessions sleysnor, 5 accessions veyzobu, 1 accession storru, 3 accessions sloysnor, 8 accessions smysnor, 1 accession smosnor, 1 accession stoyru, 4 accessions smeesnor, 1 accession smersnor, 1 accession smorsnor, 1 accession fardyby, 1 accession snosnor, 2 accessions wozobu, 1 accession sneesnor, 1 accession warzobu, 1 accession sneysnor, 1 accession snorsnor, 1 accession fordyby, 1 accession spysnor, 1 accession spusnor, 3 accessions 2 variants zeeza, 2 accessions blawsher, 1 accession speesnor, 1 accession spersnor, 2 accessions sporsnor, 1 accession spoysnor, 1 accession jydyby, 1 accession stysnor, 5 accessions stusnor, 2 accessions stosnor, 1 accession toruru, 1 accession starsnor, 2 accessions stersnor, 1 accession stoysnor, 2 accessions jerdyby, 1 accession swusnor, 1 accession swarsnor, 2 accessions plarwobu, 30 accessions leedyby, 1 accession sweesnor, 1 accession zarzobu, 1 accession choynoy, 1 accession swoysnor, 1 accession bawsnoy, 2 accessions beesnoy, 1 accession hetoma, 1 accession beero, 2 accessions berro, 6 accessions dasnoy, 1 accession chaza, 2 accessions hotoma, 3 accessions dosnoy, 1 accession deesnoy, 1 accession boyro, 1 accession dersnoy, 2 accessions wudyby, 1 accession chazobu, 1 accession daro, 8 accessions blornoy, 3 accessions fusnoy, 2 accessions farsnoy, 1 accession chawdyby, 12 accessions heturi, 2 accessions chawzobu, 1 accession feysnoy, 2 accessions foysnoy, 1 accession cheezobu, 2 accessions kloydyby, 1 accession gosnoy, 1 accession garsnoy, 3 accessions glonoy, 2 accessions CREBBP, 500 accessions 20 variants ADCY9, 137 accessions 8 variants SRL, 57 accessions, 3 variants smeysnor, 1 accession swyru, 37 accessions, 6 variants TFAP4, 97 accessions, 9 variants charglee, 2 accessions teruru, 3 accessions CORO7andTIMM16, 506 accessions 40 variants NMRAL1, 280 accessions 18 variants C16orf5, 329 accessions 14 variants FAM100A, 157 accessions 9 variants ZNF500andANKS3, 396 accessions 40 variants SEPT12, 56 accessions 9 variants flosher, 6 accessions 2 variants ROGDI, 339 accessions 15 variants siruru, 1 accession GLYR1, 398 accessions 16 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               7 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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 !