Homo sapiens gene DEPDC7, encoding DEP domain containing 7.
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SUMMARY back to top
RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .b), 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 well expressed, 0.8 times the average gene in this release. The sequence of this gene is defined by 89 GenBank accessions from 87 cDNA clones, some from testis (seen 8 times), brain (6), kidney (6), neuroblastoma cot 25-normalized (6), germinal center B cell (5), corresponding non cancerous liver tissue (4), liver (4) and 20 other tissues. We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 9 distinct gt-ag introns. Transcription produces 6 different mRNAs, 4 alternatively spliced variants and 2 unspliced forms. There are 2 probable alternative promotors, 3 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end.
Function: There is one article specifically referring to this gene in PubMed. Proteins are expected to localize in cytoplasm. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential: 4 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (4 complete), some containing Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) domain [Pfam], a coiled coil stretch [Psort2]. The remaining 2 mRNA variants (2 unspliced) appear not to encode good proteins. Finally proteins from this gene may be modulated by mono-methylation; 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 11, links to other databases and other names
Map: This gene DEPDC7 maps on chromosome 11, at 11p13 according to Entrez Gene. In AceView, it covers 17.70 kb, from 33037431 to 33055133 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 91614, 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 DEPDC7, TR2 or dJ85M6.4, LOC91614. It has been described as DEP domain-containing protein 7, novel 58.3 KDA protein, dJ85M6.4 (novel 58.3 KDA protein).
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Depdc7 (e=0.0).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT4G08550 (e=0.38)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
DEPDC7 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 1.10 0.45 10.1 43.2 2.19 0.42 3.33 6.65 1.26 0.45 2.52 0.89 2.19 0.39 9.41 40.3 0.48 0.17 2.52 1.45 24.8 0.32 1.18 0.27 1.55 0.63 35.1 1.66 1.18 1.78 0.22 1.10 0.48 0.96 23.2 57.1 26.6 0.59 0.63 0.45 2.90 0.59 15.3 28.5 1.18 1.18 11.6 1.55 4.71 65.5 0.36 10.1 0.42 2.90 0.55 7.64 0.55 5.79 0.63 0.83 4.71 0.34 1.91 3.10 0.96 0.89 0.55 0.96 20.2 0.16 2.52 5.79 2.05 1.78 7.64 1.55 0.89 1.18 23.2 7.64 6.65 1.45 0.63 1.78 8.19 0.16 2.52 0.72 0.45 5.04 0.59 32.8 46.3 1.35 2.52 2.52 1.10 5.40 80.7 1.78 46.3 1.18 0.34 1.10 0.27 0.45 2.90 0.32 6.21 1.10 17.6 2.52 0.39 46.3 1.78 0.68 1.66 8.19 0.45 4.10 0.51 1.66 0.55 5.79 35.1 6.21 0.63 5.40 4.10 0.48 1.10 3.10 0.83 0.63 0.68 106 2.05 10.1 0.96 0.24 8.78 26.6 0.68 1.66 0.68 2.70 3.10 70.2 1.18 2.05 1.45 1.35 1.10 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 DEPDC7 5' 3' encoded on plus strand of chromosome 11 from 33,037,431 to 33,055,133 7103 5683 4310 7069 7384 6018 8311 9752 a [NM] 22 5683 4310 7069 7384 6018 8311 9752 b [NM] 7103 5683 c 7103 d e-u f-u 1 2kb 0 144 bp exon 144 bp exon 9630 bp [gt-ag] intron 37 GenBank accessions 7066 RNA-seq supporting reads 1903 UHR pooled cells 419 Brain 162 Blood 4461 Neuroblastoma 121 Other (also 2093 Primates bodymap) 391 bp exon 1636 bp [gt-ag] intron 35 GenBank accessions 5648 RNA-seq supporting reads 1719 UHR pooled cells 410 Brain 185 Blood 3280 Neuroblastoma 54 Other (also 2120 Primates bodymap) 128 bp exon 789 bp [gt-ag] intron 24 GenBank accessions 4286 RNA-seq supporting reads 1494 UHR pooled cells 303 Brain 160 Blood 2303 Neuroblastoma 26 Other (also 1925 Primates bodymap) 190 bp exon 2585 bp [gt-ag] intron 17 GenBank accessions 7052 RNA-seq supporting reads 2197 UHR pooled cells 427 Brain 221 Blood 4144 Neuroblastoma 63 Other (also 2222 Primates bodymap) 212 bp exon 746 bp [gt-ag] intron 17 GenBank accessions 7367 RNA-seq supporting reads 2281 UHR pooled cells 501 Brain 207 Blood 4325 Neuroblastoma 53 Other (also 2142 Primates bodymap) 143 bp exon 189 bp [gt-ag] intron 22 GenBank accessions 5996 RNA-seq supporting reads 1912 UHR pooled cells 357 Brain 104 Blood 3581 Neuroblastoma 42 Other (also 2640 Primates bodymap) 126 bp exon 95 bp [gt-ag] intron 28 GenBank accessions 8283 RNA-seq supporting reads 2540 UHR pooled cells 554 Brain 158 Blood 4972 Neuroblastoma 59 Other (also 2864 Primates bodymap) 79 bp exon 294 bp [gt-ag] intron 34 GenBank accessions 9718 RNA-seq supporting reads 2903 UHR pooled cells 682 Brain 202 Blood 5871 Neuroblastoma 60 Other (also 3150 Primates bodymap) 321 bp exon 68 accessions, NM_001077242.1 some from kidney (seen 6 times) neuroblastoma cot 25-normalized (6) germinal center B cell (5) testis (4), corresponding non cancerous liver tissue (3) capped 5' end, 4 accessions Validated 3' end, 1 accession Validated 3' end, 4 accessions 321 bp exon 507 bp exon 507 bp exon 9073 bp [gt-ag] intron 8 GenBank accessions 14 RNA-seq supporting reads 1 Brain 13 Neuroblastoma (also 23 Primates bodymap) 391 bp exon 1636 bp [gt-ag] intron 35 GenBank accessions 5648 RNA-seq supporting reads 1719 UHR pooled cells 410 Brain 185 Blood 3280 Neuroblastoma 54 Other (also 2120 Primates bodymap) 128 bp exon 789 bp [gt-ag] intron 24 GenBank accessions 4286 RNA-seq supporting reads 1494 UHR pooled cells 303 Brain 160 Blood 2303 Neuroblastoma 26 Other (also 1925 Primates bodymap) 190 bp exon 2585 bp [gt-ag] intron 17 GenBank accessions 7052 RNA-seq supporting reads 2197 UHR pooled cells 427 Brain 221 Blood 4144 Neuroblastoma 63 Other (also 2222 Primates bodymap) 212 bp exon 746 bp [gt-ag] intron 17 GenBank accessions 7367 RNA-seq supporting reads 2281 UHR pooled cells 501 Brain 207 Blood 4325 Neuroblastoma 53 Other (also 2142 Primates bodymap) 143 bp exon 189 bp [gt-ag] intron 22 GenBank accessions 5996 RNA-seq supporting reads 1912 UHR pooled cells 357 Brain 104 Blood 3581 Neuroblastoma 42 Other (also 2640 Primates bodymap) 126 bp exon 95 bp [gt-ag] intron 28 GenBank accessions 8283 RNA-seq supporting reads 2540 UHR pooled cells 554 Brain 158 Blood 4972 Neuroblastoma 59 Other (also 2864 Primates bodymap) 79 bp exon 294 bp [gt-ag] intron 34 GenBank accessions 9718 RNA-seq supporting reads 2903 UHR pooled cells 682 Brain 202 Blood 5871 Neuroblastoma 60 Other (also 3150 Primates bodymap) 319 bp exon 9 accessions, NM_139160.2 some from testis (seen 3 times) brain (2), medulla (2) Validated 3' end, 2 accessions 319 bp exon 117 bp exon 117 bp exon 9630 bp [gt-ag] intron 37 GenBank accessions 7066 RNA-seq supporting reads 1903 UHR pooled cells 419 Brain 162 Blood 4461 Neuroblastoma 121 Other (also 2093 Primates bodymap) 391 bp exon 1636 bp [gt-ag] intron 35 GenBank accessions 5648 RNA-seq supporting reads 1719 UHR pooled cells 410 Brain 185 Blood 3280 Neuroblastoma 54 Other (also 2120 Primates bodymap) 609 bp exon 2 accessions, some from substantia nigra (seen once) testis (once) Validated 3' end, 1 accession 609 bp exon 144 bp exon 144 bp exon 9630 bp [gt-ag] intron 37 GenBank accessions 7066 RNA-seq supporting reads 1903 UHR pooled cells 419 Brain 162 Blood 4461 Neuroblastoma 121 Other (also 2093 Primates bodymap) 1059 bp exon 3 accessions, some from brain (seen 2 times) liver, tumor tissue (once) 1059 bp exon 718 bp exon 718 bp exon 3 accessions, some from liver (seen 2 times) hepatocellular carcinoma (once) 718 bp exon 321 bp exon 321 bp exon 1 accession from liver 321 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 1734 bp 511 aa 71 bp 127 bp 2kb including Promoter 17698 bp 1kb
bAug10 2095 bp 502 aa 461 bp 125 bp 2kb possibly including promoter 17502 bp 1kb
cAug10 1117 bp 207 aa 44 bp 449 bp 2kb probably including promoter 12383 bp 1kb
dAug10 1203 bp 190 aa 71 bp 559 bp 2kb probably including promoter 10833 bp 1kb
eAug10-unspliced 718 bp 54 aa 215 bp 338 bp 2kb 718 bp 1kb
fAug10-unspliced 321 bp 14 aa 160 bp 116 bp 2kb 321 bp 1kb

Gene neighbors and Navigator on chromosome 11p13 back to top
EIF3M D C I R P PRRG4 D C R P QSER1 D C R P DEPDC7 C R P TCP11L1 C R P G C C C G R HIPK3 D C I R P C RPS24P15 C R P CCDC73 P C I R P CSTF3 100kb 0 EIF3M, 429 accessions 19 variants PRRG4, 72 accessions, 3 variants QSER1, 266 accessions 9 variants DEPDC7, 87 accessions 6 variants TCP11L1, 141 accessions 16 variants LOC283267, 110 accessions seefee, 1 accession hikura, 16 accessions LOC338739, 10 accessions 2 variants HIPK3, 246 accessions 6 variants peeflorbu, 1 accession lerflorbu, 1 accession dorlyby, 2 accessions leyflorbu, 1 accession falyby, 2 accessions lorflorbu, 1 accession farlyby, 1 accession fawlyby, 1 accession feelyby, 1 accession feylyby, 2 accessions forlyby, 1 accession foylyby, 2 accessions myflorbu, 2 accessions smawsmeeby, 1 accession galyby, 3 accessions swortubo, 7 accessions muflorbu, 1 accession glerflobu, 5 accessions gulyby, 1 accession golyby, 2 accessions faklu, 1 accession garlyby, 1 accession moflorbu, 1 accession marflorbu, 1 accession mawflorbu, 2 accessions notomi, 1 accession gawlyby, 1 accession meeflorbu, 1 accession meyflorbu, 1 accession geelyby, 1 accession geylyby, 1 accession goylyby, 1 accession jalyby, 1 accession sarfee, 2 accessions jylyby, 1 accession julyby, 1 accession jolyby, 1 accession snosmeeby, 2 accessions jeelyby, 2 accessions speesmeeby, 1 accession goyklu, 2 accessions jerlyby, 4 accessions jorlyby, 1 accession joylyby, 1 accession sweysmeeby, 2 accessions keelyby, 2 accessions 2 variants neeflorbu, 1 accession smerchee, 1 accession terure, 2 accessions lerklu, 1 accession RPS24P15, 2 accessions parflorbu, 1 accession marlyby, 2 accessions mawlyby, 2 accessions pawflorbu, 1 accession meelyby, 1 accession meylyby, 3 accessions dusmerby, 16 accessions moylyby, 2 accessions nalyby, 1 accession garfeyby, 3 accessions geysmerby, 2 accessions porflorbu, 4 accessions nolyby, 1 accession naklu, 1 accession gorsmerby, 1 accession nuklu, 1 accession raflorbu, 2 accessions norlyby, 1 accession palyby, 1 accession korsmerby, 1 accession lysmerby, 1 accession ruflorbu, 1 accession sneemaw, 9 accessions roflorbu, 1 accession parlyby, 1 accession bawtobo, 3 accessions rarflorbu, 3 accessions peylyby, 1 accession poylyby, 1 accession ralyby, 1 accession snychee, 1 accession rulyby, 1 accession tatomi, 2 accessions, 2 variants reeflorbu, 1 accession lorsmerby, 1 accession rawlyby, 1 accession gloysmeeby, 1 accession dawlyby, 1 accession deelyby, 1 accession derlyby, 2 accessions deylyby, 1 accession doylyby, 1 accession loyflorbu, 1 accession maflorbu, 1 accession fulyby, 1 accession skawsmeeby, 1 accession folyby, 1 accession sleysmeeby, 2 accessions doyklu, 1 accession merflorbu, 1 accession safee, 4 accessions gerlyby, 1 accession gorlyby, 1 accession morflorbu, 1 accession batobo, 1 accession yamuro, 1 accession wergerby, 1 accession feeklu, 1 accession jarlyby, 1 accession jawlyby, 1 accession geyklu, 2 accessions kalyby, 2 accessions kylyby, 1 accession kulyby, 1 accession nyflorbu, 1 accession karlyby, 1 accession kawlyby, 1 accession nuflorbu, 1 accession smeechee, 2 accessions kawklu, 1 accession basmerby, 1 accession bytobo, 1 accession keylyby, 1 accession dasmerby, 1 accession blagerby, 4 accessions koylyby, 1 accession lalyby, 1 accession dysmerby, 2 accessions nerflorbu, 1 accession neyflorbu, 1 accession norflorbu, 1 accession lolyby, 1 accession noyflorbu, 1 accession lawlyby, 1 accession kerklu, 2 accessions lerlyby, 1 accession leylyby, 1 accession pyflorbu, 1 accession muklu, 1 accession butobo, 1 accession merklu, 2 accessions gleygerby, 1 accession morlyby, 1 accession fysmerby, 2 accessions gusmerby, 1 accession snachee, 1 accession nulyby, 3 accessions bartobo, 1 accession narlyby, 1 accession nawlyby, 1 accession neelyby, 1 accession poyflorbu, 1 accession noylyby, 1 accession pulyby, 1 accession ryflorbu, 1 accession pawlyby, 1 accession perlyby, 1 accession porlyby, 1 accession skoygerby, 1 accession rawflorbu, 1 accession rylyby, 1 accession leesmerby, 1 accession rolyby, 1 accession meesmerby, 1 accession reelyby, 1 accession CCDC73, 26 accessions 3 variants yuha, 1 accession CSTF3, 431 accessions 18 variants 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 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 !