Homo sapiens complex locus RAB25, encoding RAB25, member RAS oncogene family.
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SUMMARY back to top
RefSeq summary
[RAB25] RAB proteins, such as RAB25, are members of the RAS superfamily of small GTPases that are involved in membrane trafficking. Members of the RAB11 subfamily, including RAB25, control the return of internalized membrane-associated moieties to the cell surface (Caswell et al., 2007 [PubMed 17925226]).[supplied by OMIM].

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 6 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at high level, 2.4 times the average gene in this release. The sequence of this gene is defined by 273 GenBank accessions from 247 cDNA clones, some from colon (seen 27 times), head neck (24), ovary (17), stomach (17), prostate (15), breast (14), lung (13) and 81 other tissues. We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 6 distinct gt-ag introns. Transcription produces 6 alternatively spliced mRNAs. 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 5' end, truncation of the 3' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries.
Function: There are 14 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Adenocarcinoma; Barrett Esophagus; Breast Neoplasms; Cell Transformation, Neoplastic; Colorectal Neoplasms; Ovarian Neoplasms) and proposed to participate in processes (positive regulation of cell proliferation, pseudopodium organization, protein transport, small GTPase mediated signal transduction). Proteins are expected to have molecular functions (identical protein binding, GTP binding, nucleotide binding) and to localize in various compartments (cytoplasm, cytoplasmic vesicle, plasma membrane, pseudopodium, cytoplasmic membrane-bounded vesicle, pseudopodium membrane). Putative protein interactors have been described (ACVR1, AP2S1, BMPR1B, ELAC1ANDSMAD4, KPTN, MED31, MYO5BANDACAA2, PKIG, RAB11FIP1, RAB11FIP2, RAB11FIP3, RAB11FIP5, SMURF2, TGFBR1).
Protein coding potential: 5 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (3 complete, 1 partial), some containing domains Miro-like protein, Ras family [Pfam]. The remaining mRNA variant (spliced) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 1, links to other databases and other names
Map: This gene RAB25 maps on chromosome 1, at 1q22 according to Entrez Gene. In AceView, it covers 9.37 kb, from 156030940 to 156040304 (NCBI 37, August 2010), on the direct strand.
Links to: the SNP view, gene overviews from Entrez Gene 57111, 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 RAB25, CATX-8 or RAB11C, LOC57111. It has been described as ras-related protein Rab-25.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Rab25 (e=3 10-77).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene rab-11.1 (e=5 10-51), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes AtRABA1i (e=2 10-51), AtRABA1e (e=2 10-50), AtRABA1g (e=5 10-50), 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
RAB25 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 18.8 0.42 15.3 0.68 1.02 1.18 0.11 16.4 24.8 0.89 18.8 4.39 2.70 0.34 1.55 15.3 0.63 4.10 0.27 0.34 0.42 4.10 0.19 0.18 92.7 0.16 13.3 0.18 0.24 0.22 0.55 1.91 2.05 0.55 11.6 13.3 0.63 0.21 0.27 65.5 0.48 0.34 0.21 0.21 5.79 15.3 0.59 0.26 0.16 17.6 10.8 11.6 0.32 4.71 0.45 0.51 86.5 3.57 8.19 12.4 2.35 0.24 7.64 0.27 86.5 0.22 4.71 35.1 0.16 14.3 0.45 7.13 0.22 1.66 0.26 8.19 8.19 0.22 0.72 10.8 1.45 57.1 0.39 0.55 7.64 14.3 0.59 8.78 0.18 2.05 61.1 2.70 0.22 0.16 0.11 8.78 0.55 0.18 0.55 70.2 5.79 7.13 8.78 6.21 0.68 18.8 0.63 16.4 24.8 9.41 0.34 11.6 2.90 6.21 2.52 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 RAB25 5' 3' encoded on plus strand of chromosome 1 from 156,030,940 to 156,040,304 4101 4150 6614 6940 a [NM] 4101 179 6614 b 614 6614 6940 c 4101 e 6614 6940 d 614 6614 f 1kb 0 295 bp exon 295 bp exon 4467 bp [gt-ag] intron 96 GenBank accessions 4005 RNA-seq supporting reads 3121 UHR pooled cells 69 Brain 77 Blood 727 Neuroblastoma 11 Other (also 2046 Primates bodymap) 196 bp exon 2163 bp [gt-ag] intron 91 GenBank accessions 4059 RNA-seq supporting reads 3330 UHR pooled cells 97 Brain 69 Blood 558 Neuroblastoma 5 Other (also 1444 Primates bodymap) 194 bp exon 1207 bp [gt-ag] intron 143 GenBank accessions 6471 RNA-seq supporting reads 4772 UHR pooled cells 210 Brain 109 Blood 1371 Neuroblastoma 9 Other (also 2040 Primates bodymap) 81 bp exon 408 bp [gt-ag] intron 147 GenBank accessions 6793 RNA-seq supporting reads 5055 UHR pooled cells 229 Brain 77 Blood 1419 Neuroblastoma 13 Other (also 2303 Primates bodymap) 354 bp exon 163 accessions, NM_020387.2 some from stomach (seen 13 times) colon (12), ovary (11) prostate (11), breast (10) Validated 3' end, 15 accessions Validated 3' end, 6 accessions 354 bp exon 269 bp exon 269 bp exon 4467 bp [gt-ag] intron 96 GenBank accessions 4005 RNA-seq supporting reads 3121 UHR pooled cells 69 Brain 77 Blood 727 Neuroblastoma 11 Other (also 2046 Primates bodymap) 175 bp exon 2184 bp [gt-ag] intron 2 GenBank accessions 177 RNA-seq supporting reads 147 UHR pooled cells 6 Brain 3 Blood 21 Neuroblastoma (also 21 Primates bodymap) 194 bp exon 1207 bp [gt-ag] intron 143 GenBank accessions 6471 RNA-seq supporting reads 4772 UHR pooled cells 210 Brain 109 Blood 1371 Neuroblastoma 9 Other (also 2040 Primates bodymap) 2 accessions, some from colon (seen once) embryonic stem cells dmso-treated H9 cellline (once) 23 bp exon 263 bp exon 6826 bp [gt-ag] intron 20 GenBank accessions 594 RNA-seq supporting reads 473 UHR pooled cells 10 Brain 7 Blood 103 Neuroblastoma 1 Other (also 471 Primates bodymap) 194 bp exon 194 bp exon 1207 bp [gt-ag] intron 143 GenBank accessions 6471 RNA-seq supporting reads 4772 UHR pooled cells 210 Brain 109 Blood 1371 Neuroblastoma 9 Other (also 2040 Primates bodymap) 81 bp exon 408 bp [gt-ag] intron 147 GenBank accessions 6793 RNA-seq supporting reads 5055 UHR pooled cells 229 Brain 77 Blood 1419 Neuroblastoma 13 Other (also 2303 Primates bodymap) 346 bp exon 15 accessions, some from stomach (seen 4 times) lymph node (3), ovary (3) adenocarcinoma cell line (2) adenocarcinoma (once) Validated 3' end, 1 accession 346 bp exon 263 bp exon 263 bp exon 45 bp uORF 263 bp exon 263 bp exon 4467 bp [gt-ag] intron 96 GenBank accessions 4005 RNA-seq supporting reads 3121 UHR pooled cells 69 Brain 77 Blood 727 Neuroblastoma 11 Other (also 2046 Primates bodymap) 372 bp exon 372 bp exon 3 accessions, some from colon (seen once) eye (once), lacrimal gland (once) trachea (once) capped 5' end, 1 accession 372 bp exon 299 bp exon 299 bp exon 96 bp uORF 299 bp exon 299 bp exon 1207 bp [gt-ag] intron 143 GenBank accessions 6471 RNA-seq supporting reads 4772 UHR pooled cells 210 Brain 109 Blood 1371 Neuroblastoma 9 Other (also 2040 Primates bodymap) 81 bp exon 81 bp exon 408 bp [gt-ag] intron 147 GenBank accessions 6793 RNA-seq supporting reads 5055 UHR pooled cells 229 Brain 77 Blood 1419 Neuroblastoma 13 Other (also 2303 Primates bodymap) 354 bp exon 354 bp exon 65 accessions, some from colon (seen 13 times) head neck (13), lung (5) pooled human melanocyte fetal heart, andpregnant uterus (5) breast (3) Validated 3' end, 10 accessions 354 bp exon 284 bp exon 6826 bp [gt-ag] intron 20 GenBank accessions 594 RNA-seq supporting reads 473 UHR pooled cells 10 Brain 7 Blood 103 Neuroblastoma 1 Other (also 471 Primates bodymap) 194 bp exon 194 bp exon 1207 bp [gt-ag] intron 143 GenBank accessions 6471 RNA-seq supporting reads 4772 UHR pooled cells 210 Brain 109 Blood 1371 Neuroblastoma 9 Other (also 2040 Primates bodymap) 430 bp exon 5 accessions, some from astrocytoma grade IV cell line (seen once) brain (once), epidermis (once) rectum (once) 430 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 1120 bp 213 aa 252 bp 226 bp 2kb probably including promoter 9365 bp 1kb
bAug10 661 bp 145 aa 226 bp 2kb probably including promoter 8519 bp 1kb
cAug10 884 bp 93 aa 384 bp 218 bp 2kb probably including promoter 9325 bp 1kb
dAug10 734 bp 93 aa 226 bp 226 bp 93 bp 2kb possibly including promoter 2349 bp 1kb
eAug10 635 bp 80 aa 220 bp 172 bp 42 bp 2kb including Promoter 5102 bp 1kb
fAug10 908 bp 53 aa 376 bp 370 bp 2kb probably including promoter 8941 bp 1kb

Gene neighbors and Navigator on chromosome 1q22 back to top
D C R P DAP3 D C I R P C MSTO2P C R P SYT11 D C I R P RXFP4 C I P R ROBLD3 D C I R P RAB25 D C I R P LMNA D C I R P C SEMA4A D C I R P SLC25A44 C R P C PMF1andBGLAP D C I R P R TMEM79 C R P C1orf182 C I R RHBG C R P SCARNA4 G C R C R C D C I R P YY1AP1 R C R P GON4L D C I R P RIT1 C I R P KIAA0907 P SNORA42 D C I R P ARHGEF2 C I R P SSR2 C I R P MEX3AandUBQLN4 R P C R P PAQR6 C I R P SMG5 C R P C1orf85 C I P VHLL C I R P CCT3 C C I R P C1orf61 C I R P MEF2D C R P IQGAP3 100kb 0 MRPS29P1andMSTO1, 436 accessions 33 variants DAP3, 471 accessions, 33 variants flureebu, 1 accession MSTO2P, 335 accessions 33 variants SYT11, 239 accessions 5 variants RXFP4, 19 accessions klyler, 6 accessions, 3 variants ROBLD3, 206 accessions 9 variants RAB25, 257 accessions 6 variants LMNA, 675 accessions, 26 variants gleygeebu, 3 accessions SEMA4A, 283 accessions 27 variants SLC25A44, 409 accessions 16 variants tekayo, 1 accession PMF1andBGLAP, 475 accessions 20 variants kloyler, 2 accessions TMEM79, 194 accessions 10 variants C1orf182, 89 accessions 11 variants RHBG, 35 accessions, 14 variants plorerbo, 2 accessions puplaw, 1 accession seegeebu, 14 accessions derkawbo, 1 accession skurerbo, 1 accession choreebu, 2 accessions deykawbo, 2 accessions japoybo, 1 accession rusemo, 2 accessions, 2 variants skarrerbo, 2 accessions cheereebu, 1 accession choyreebu, 1 accession shureebu, 3 accessions fokawbo, 1 accession jarpoybo, 2 accessions foykawbo, 2 accessions blarreebu, 2 accessions jerpoybo, 1 accession takayo, 1 accession sorgeebu, 1 accession gykawbo, 2 accessions flareebu, 2 accessions slyrerbo, 3 accessions kopoybo, 1 accession slurerbo, 1 accession slorerbo, 1 accession parvoybo, 4 accessions gerkawbo, 5 accessions florreebu, 1 accession smorerbo, 1 accession pawvoybo, 1 accession goykawbo, 1 accession glyreebu, 1 accession smawrerbo, 2 accessions glarreebu, 3 accessions gleereebu, 2 accessions jawkawbo, 2 accessions gleyreebu, 1 accession peevoybo, 1 accession miya, 9 accessions soygeebu, 1 accession klareebu, 1 accession jeykawbo, 1 accession jorkawbo, 1 accession kloreebu, 2 accessions klawreebu, 1 accession kleyreebu, 1 accession plyreebu, 2 accessions resemo, 3 accessions ploreebu, 1 accession snarerbo, 1 accession keykawbo, 3 accessions vorgeebu, 1 accession skoreebu, 1 accession snerrerbo, 1 accession skawreebu, 5 accessions skerreebu, 1 accession lerpoybo, 1 accession weybaw, 4 accessions skorreebu, 2 accessions skoyreebu, 1 accession chergeebu, 1 accession floygeebu, 2 accessions snoyrerbo, 1 accession sloreebu, 1 accession lykawbo, 4 accessions sleyreebu, 1 accession slorreebu, 1 accession sloyreebu, 1 accession smyreebu, 6 accessions lokawbo, 1 accession tikayo, 1 accession smureebu, 2 accessions smoreebu, 2 accessions mapoybo, 6 accessions voypla, 4 accessions smarreebu, 2 accessions sparrerbo, 1 accession smawreebu, 1 accession smerreebu, 2 accessions kloler, 3 accessions glawgeebu, 1 accession wypla, 2 accessions snyreebu, 2 accessions speererbo, 1 accession tukayo, 1 accession sporrerbo, 2 accessions lorkawbo, 5 accessions sneyreebu, 1 accession mopoybo, 3 accessions spyreebu, 2 accessions mokawbo, 2 accessions spureebu, 3 accessions ruvoybo, 2 accessions merkawbo, 2 accessions styrerbo, 1 accession rovoybo, 1 accession speyreebu, 2 accessions stareebu, 2 accessions plovu, 11 accessions starreebu, 3 accessions stawreebu, 1 accession weepla, 2 accessions morpoybo, 5 accessions steyreebu, 5 accessions sherpeybo, 1 accession sturerbo, 1 accession smergeebu, 1 accession stoyreebu, 1 accession smeygeebu, 1 accession narkawbo, 1 accession sworeebu, 2 accessions sweereebu, 5 accessions nopoybo, 1 accession snoygeebu, 6 accessions sworreebu, 3 accessions swoyreebu, 2 accessions starrerbo, 1 accession parkawbo, 1 accession rosemo, 2 accessions, 2 variants hiya, 2 accessions yasemo, 1 accession barrerbu, 1 accession stawrerbo, 1 accession neepoybo, 2 accessions berrerbu, 1 accession beyrerbu, 1 accession spergeebu, 3 accessions dyrerbu, 1 accession perkawbo, 1 accession sterrerbo, 3 accessions derrerbu, 1 accession dorrerbu, 2 accessions doyrerbu, 3 accessions stoyrerbo, 1 accession zypla, 3 accessions plawrerbo, 2 accessions chyreebu, 1 accession plerrerbo, 1 accession chureebu, 3 accessions bloyreebu, 1 accession charreebu, 3 accessions yaya, 4 accessions skeyrerbo, 1 accession shoreebu, 2 accessions fukawbo, 1 accession ferkawbo, 7 accessions forkawbo, 2 accessions sherreebu, 1 accession pawplaw, 1 accession sheyreebu, 2 accessions peeplaw, 8 accessions jawpoybo, 5 accessions blyreebu, 2 accessions blureebu, 1 accession bloreebu, 1 accession blawreebu, 1 accession blorreebu, 1 accession kypoybo, 1 accession gukawbo, 1 accession gokawbo, 3 accessions flyreebu, 1 accession fleereebu, 2 accessions fleyreebu, 1 accession koypoybo, 1 accession smarrerbo, 1 accession glareebu, 1 accession glawler, 1 accession jakawbo, 1 accession jokawbo, 1 accession glawreebu, 1 accession glorler, 3 accessions jeekawbo, 1 accession glerreebu, 1 accession joykawbo, 1 accession klureebu, 1 accession kokawbo, 1 accession vugeebu, 1 accession lypoybo, 4 accessions kawkawbo, 1 accession SCARNA4, 2 accessions smerrerbo, 1 accession peyvoybo, 1 accession porvoybo, 1 accession plawreebu, 3 accessions snarrerbo, 1 accession pleereebu, 1 accession plerreebu, 1 accession pleyreebu, 2 accessions korkawbo, 1 accession ployreebu, 1 accession skareebu, 1 accession klaler, 0 accession wargeebu, 1 accession flageebu, 1 accession ravoybo, 1 accession slureebu, 2 accessions slarreebu, 2 accessions slawreebu, 1 accession sparerbo, 1 accession slerreebu, 1 accession veypla, 3 accessions lukawbo, 1 accession spyrerbo, 1 accession spurerbo, 1 accession smeereebu, 1 accession smeyreebu, 1 accession smorreebu, 1 accession wapla, 11 accessions ryvoybo, 4 accessions snareebu, 1 accession gleegeebu, 1 accession leekawbo, 1 accession snyvorbo, 1 accession sneereebu, 4 accessions snerreebu, 5 accessions loykawbo, 1 accession makawbo, 2 accessions spoyrerbo, 1 accession snoyreebu, 1 accession mykawbo, 1 accession markawbo, 1 accession starerbo, 1 accession marpoybo, 3 accessions meekawbo, 1 accession morkawbo, 1 accession wawpla, 11 accessions merpoybo, 1 accession sperreebu, 1 accession skeegeebu, 1 accession styreebu, 2 accessions moykawbo, 2 accessions skergeebu, 3 accessions nukawbo, 1 accession nokawbo, 4 accessions swureebu, 3 accessions swawreebu, 2 accessions nerkawbo, 1 accession noykawbo, 2 accessions pykawbo, 1 accession bawrerbu, 2 accessions borrerbu, 1 accession pawkawbo, 1 accession darerbu, 1 accession peekawbo, 1 accession nerpoybo, 2 accessions durerbu, 1 accession rawvoybo, 1 accession dawrerbu, 1 accession woypla, 8 accessions deyrerbu, 1 accession farerbu, 1 accession swarerbo, 1 accession fyrerbu, 2 accessions poykawbo, 1 accession zupla, 1 accession LOC284620, 1 accession susamo, 47 accessions 2 variants sesamo, 17 accessions 4 variants farkawbo, 13 accessions YY1AP1, 636 accessions 38 variants voybaw, 10 accessions 3 variants GON4L, 317 accessions 25 variants RIT1, 198 accessions, 10 variants KIAA0907, 388 accessions 16 variants SNORA42, 6 accessions 2 variants ARHGEF2, 399 accessions 27 variants SSR2, 445 accessions, 17 variants MEX3AandUBQLN4, 557 accessions 12 variants mypoybo, 1 accession mito_carr.42, 2 accessions PAQR6, 721 accessions 37 variants SMG5, 458 accessions, 12 variants C1orf85, 327 accessions 16 variants VHLL, 6 accessions CCT3, 552 accessions, 27 variants barerbu, 1 accession C1orf61, 344 accessions 38 variants MEF2D, 411 accessions 13 variants IQGAP3, 146 accessions 7 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               14 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f 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'.

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