Human Gene SGSM2 (ENST00000268989.8_7) from GENCODE V47lift37

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Description: small G protein signaling modulator 2, transcript variant 1 (from RefSeq NM_014853.3)
Gencode Transcript: ENST00000268989.8_7
Gencode Gene: ENSG00000141258.13_11
Transcript (Including UTRs)
Position: hg19 chr17:2,240,795-2,284,348 Size: 43,554 Total Exon Count: 24 Strand: +
Coding Region
Position: hg19 chr17:2,240,983-2,282,814 Size: 41,832 Coding Exon Count: 24

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr17:2,240,795-2,284,348)			mRNA (may differ from genome)		Protein (1051 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	MGI	OMIM	PubMed	UniProtKB	Wikipedia
BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: SGSM2_HUMAN DESCRIPTION: RecName: Full=Small G protein signaling modulator 2; AltName: Full=RUN and TBC1 domain-containing protein 1; SUBUNIT: Interacts with RAB4A, RAB11A, RAP1A, RAP1B, RAP2A and RAP2B. No interaction with RAB27A. TISSUE SPECIFICITY: Widely expressed. SIMILARITY: Belongs to the RUTBC family. SIMILARITY: Contains 1 Rab-GAP TBC domain. SIMILARITY: Contains 1 RUN domain. SEQUENCE CAUTION: Sequence=BAA23693.3; Type=Erroneous initiation;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D016604 Aflatoxin B1 D002251 Carbon Tetrachloride D013749 Tetrachlorodibenzodioxin D014635 Valproic Acid D014810 Vitamin E C044887 beta-methylcholine C069837 fullerene C60 C028007 nickel monoxide C006253 pirinixic acid

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 88.83 RPKM in Pituitary Total median expression: 1483.26 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-110.30	188	-0.587	Picture	PostScript	Text
3' UTR	-657.50	1534	-0.429	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR000195 - Rab-GTPase-TBC_dom
IPR004012 - Run

Pfam Domains:
PF00566 - Rab-GTPase-TBC domain
PF02759 - RUN domain
PF12068 - Rab-binding domain (RBD)

SCOP Domains:
140741 - RUN domain-like
47923 - Ypt/Rab-GAP domain of gyp1p

ModBase Predicted Comparative 3D Structure on O43147


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0005096 GTPase activator activity GO:0017137 Rab GTPase binding Biological Process: GO:0006886 intracellular protein transport GO:0031338 regulation of vesicle fusion GO:0034499 late endosome to Golgi transport GO:0043547 positive regulation of GTPase activity GO:0090630 activation of GTPase activity Cellular Component: GO:0005737 cytoplasm GO:0012505 endomembrane system GO:0042470 melanosome

Descriptions from all associated GenBank mRNAs


	LF384765 - JP 2014500723-A/192268: Polycomb-Associated Non-Coding RNAs. AB007857 - Homo sapiens KIAA0397 mRNA for KIAA0397 protein. BC039204 - Homo sapiens small G protein signaling modulator 2, mRNA (cDNA clone MGC:26223 IMAGE:4817100), complete cds. AK294955 - Homo sapiens cDNA FLJ60111 complete cds, highly similar to Homo sapiens RUN and TBC1 domain containing 1 (RUTBC1), mRNA. AB275762 - Homo sapiens SGSM2 mRNA for small G protein signaling modulator 2 protein, complete cds. AB385325 - Synthetic construct DNA, clone: pF1KA0397, Homo sapiens O43147-2 gene for RUN and TBC1 domain-containing protein 1 isoform 1, complete cds, without stop codon, in Flexi system. KJ904638 - Synthetic construct Homo sapiens clone ccsbBroadEn_14032 SGSM2-like gene, encodes complete protein. AB449878 - Homo sapiens RUTBC1 mRNA for RUN and TBC1 domain-containing protein 1, complete cds. AK304263 - Homo sapiens cDNA FLJ57442 complete cds, highly similar to Homo sapiens RUN and TBC1 domain containing 1 (RUTBC1), mRNA. DL137704 - Novel nucleic acids. JA611268 - Sequence 32 from Patent EP2374884. AK124883 - Homo sapiens cDNA FLJ42893 fis, clone BRHIP3008598. AK125203 - Homo sapiens cDNA FLJ43213 fis, clone FEBRA2021339. BC029251 - Homo sapiens small G protein signaling modulator 2, mRNA (cDNA clone IMAGE:5170306), with apparent retained intron. BC040590 - Homo sapiens small G protein signaling modulator 2, mRNA (cDNA clone IMAGE:5269706), ** WARNING: chimeric clone **. JD382761 - Sequence 363785 from Patent EP1572962. JD449489 - Sequence 430513 from Patent EP1572962. JD544047 - Sequence 525071 from Patent EP1572962. JD079216 - Sequence 60240 from Patent EP1572962. JD165565 - Sequence 146589 from Patent EP1572962. JD050323 - Sequence 31347 from Patent EP1572962. JD051140 - Sequence 32164 from Patent EP1572962. JD130463 - Sequence 111487 from Patent EP1572962. JD059966 - Sequence 40990 from Patent EP1572962. JD324384 - Sequence 305408 from Patent EP1572962. JD426436 - Sequence 407460 from Patent EP1572962. JD520063 - Sequence 501087 from Patent EP1572962. JD127317 - Sequence 108341 from Patent EP1572962. JD360060 - Sequence 341084 from Patent EP1572962. JD162975 - Sequence 143999 from Patent EP1572962. JD381798 - Sequence 362822 from Patent EP1572962. JD381799 - Sequence 362823 from Patent EP1572962. JD326404 - Sequence 307428 from Patent EP1572962. JD186752 - Sequence 167776 from Patent EP1572962. JD185605 - Sequence 166629 from Patent EP1572962. JD167532 - Sequence 148556 from Patent EP1572962. JD160281 - Sequence 141305 from Patent EP1572962. JD062862 - Sequence 43886 from Patent EP1572962. BC061895 - Homo sapiens cDNA clone IMAGE:4441880, partial cds. JD441932 - Sequence 422956 from Patent EP1572962. JD330242 - Sequence 311266 from Patent EP1572962. JD174550 - Sequence 155574 from Patent EP1572962. JD060155 - Sequence 41179 from Patent EP1572962. JD423259 - Sequence 404283 from Patent EP1572962. JD212067 - Sequence 193091 from Patent EP1572962. JD110451 - Sequence 91475 from Patent EP1572962. JD508681 - Sequence 489705 from Patent EP1572962. JD455958 - Sequence 436982 from Patent EP1572962. JD123504 - Sequence 104528 from Patent EP1572962. JD424699 - Sequence 405723 from Patent EP1572962. JD389787 - Sequence 370811 from Patent EP1572962. JD125818 - Sequence 106842 from Patent EP1572962. JD494126 - Sequence 475150 from Patent EP1572962. JD484575 - Sequence 465599 from Patent EP1572962. JD115825 - Sequence 96849 from Patent EP1572962. JD403291 - Sequence 384315 from Patent EP1572962. JD276043 - Sequence 257067 from Patent EP1572962. JD413980 - Sequence 395004 from Patent EP1572962. MA620342 - JP 2018138019-A/192268: Polycomb-Associated Non-Coding RNAs.

Other Names for This Gene


	Alternate Gene Symbols: A5LGW2, B4DH69, ENST00000268989.1, ENST00000268989.2, ENST00000268989.3, ENST00000268989.4, ENST00000268989.5, ENST00000268989.6, ENST00000268989.7, KIAA0397, NM_014853, O43147, Q49AC2, Q6ZUY2, Q8IXU4, RUTBC1, SGSM2_HUMAN, uc317ipk.1, uc317ipk.2 UCSC ID: ENST00000268989.8_7 RefSeq Accession: NM_014853.3 Protein: O43147 (aka SGSM2_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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