Human Gene SYNJ2BP-COX16 (uc021rvn.1) Description and Page Index
  Description: Homo sapiens SYNJ2BP-COX16 readthrough (SYNJ2BP-COX16), transcript variant 1, mRNA.
RefSeq Summary (NM_001202547): This locus represents naturally occurring read-through transcription between the neighboring SYNJ2BP (synaptojanin 2 binding protein) and COX16 (COX16 cytochrome c oxidase assembly homolog (S. cerevisiae)) genes on chromosome 14. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. Alternate splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, Feb 2011].
Transcript (Including UTRs)
   Position: hg19 chr14:70,791,798-70,883,807 Size: 92,010 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr14:70,793,050-70,883,680 Size: 90,631 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:70,791,798-70,883,807)mRNA (may differ from genome)Protein (191 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHPRDLynxMGIneXtProtPubMed
Stanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SYJ2B_HUMAN
DESCRIPTION: RecName: Full=Synaptojanin-2-binding protein; AltName: Full=Mitochondrial outer membrane protein 25;
SUBUNIT: Binds (via the PDZ domain) to isoform 2A of SYNJ2 (via the unique motif in the C-terminus) (By similarity). Interacts with MAPK12 (By similarity).
SUBCELLULAR LOCATION: Mitochondrion outer membrane (By similarity).
SIMILARITY: Contains 1 PDZ (DHR) domain.

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.58 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 719.20 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
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.20127-0.285 Picture PostScript Text
3' UTR -303.501252-0.242 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
IPR001478 - PDZ

Pfam Domains:
PF00595 - PDZ domain (Also known as DHR or GLGF)
PF13180 - PDZ domain
PF14138 - Cytochrome c oxidase assembly protein COX16

SCOP Domains:
50156 - PDZ domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2ENO
- NMR MuPIT

2JIK
- X-ray MuPIT

2JIN
- X-ray


ModBase Predicted Comparative 3D Structure on P57105
FrontTopSide
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008022 protein C-terminus binding

Biological Process:
GO:0001937 negative regulation of endothelial cell proliferation
GO:0006605 protein targeting
GO:0007266 Rho protein signal transduction
GO:0008593 regulation of Notch signaling pathway
GO:0010596 negative regulation of endothelial cell migration
GO:0016525 negative regulation of angiogenesis
GO:0030100 regulation of endocytosis
GO:0048312 intracellular distribution of mitochondria
GO:0070373 negative regulation of ERK1 and ERK2 cascade
GO:1903671 negative regulation of sprouting angiogenesis

Cellular Component:
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031307 integral component of mitochondrial outer membrane


-  Descriptions from all associated GenBank mRNAs
  FJ460510 - Homo sapiens cytochrome c oxidase assembly factor isoform 1 mRNA, complete cds.
JD513286 - Sequence 494310 from Patent EP1572962.
JD293354 - Sequence 274378 from Patent EP1572962.
JD428339 - Sequence 409363 from Patent EP1572962.
JD153623 - Sequence 134647 from Patent EP1572962.
JD326026 - Sequence 307050 from Patent EP1572962.
AF226729 - Homo sapiens PTD019 mRNA, complete cds.
FJ460511 - Homo sapiens cytochrome c oxidase assembly factor isoform 2 mRNA, complete cds.
JD242138 - Sequence 223162 from Patent EP1572962.
AF151037 - Homo sapiens HSPC203 mRNA, complete cds.
AX810696 - Sequence 20 from Patent EP1333092.
BC001702 - Homo sapiens COX16 cytochrome c oxidase assembly homolog (S. cerevisiae), mRNA (cDNA clone MGC:887 IMAGE:2966935), complete cds.
JD084061 - Sequence 65085 from Patent EP1572962.
AK290743 - Homo sapiens cDNA FLJ76547 complete cds.
LF329869 - JP 2014500723-A/137372: Polycomb-Associated Non-Coding RNAs.
JD502929 - Sequence 483953 from Patent EP1572962.
HQ448730 - Synthetic construct Homo sapiens clone IMAGE:100072176; CCSB006088_02 chromosome 14 open reading frame 112 (C14orf112) gene, encodes complete protein.
KJ893858 - Synthetic construct Homo sapiens clone ccsbBroadEn_03252 COX16 gene, encodes complete protein.
CR457199 - Homo sapiens full open reading frame cDNA clone RZPDo834G068D for gene C14orf112, chromosome 14 open reading frame 112; complete cds, incl. stopcodon.
AB528661 - Synthetic construct DNA, clone: pF1KB6757, Homo sapiens COX16 gene for COX16 cytochrome c oxidase assembly homolog, without stop codon, in Flexi system.
CU674840 - Synthetic construct Homo sapiens gateway clone IMAGE:100017903 5' read C14orf112 mRNA.
LF329870 - JP 2014500723-A/137373: Polycomb-Associated Non-Coding RNAs.
AY534623 - Homo sapiens activin receptor interacting protein 5 mRNA, complete cds.
AK002133 - Homo sapiens cDNA FLJ11271 fis, clone PLACE1009319, moderately similar to Rattus norvegicus outer membrane protein mRNA.
AK311719 - Homo sapiens cDNA, FLJ18761.
LF210494 - JP 2014500723-A/17997: Polycomb-Associated Non-Coding RNAs.
BC007704 - Homo sapiens synaptojanin 2 binding protein, mRNA (cDNA clone MGC:10277 IMAGE:3952366), complete cds.
KJ899128 - Synthetic construct Homo sapiens clone ccsbBroadEn_08522 SYNJ2BP gene, encodes complete protein.
AB527912 - Synthetic construct DNA, clone: pF1KB0931, Homo sapiens SYNJ2BP gene for synaptojanin 2 binding protein, without stop codon, in Flexi system.
LF329883 - JP 2014500723-A/137386: Polycomb-Associated Non-Coding RNAs.
LF338275 - JP 2014500723-A/145778: Polycomb-Associated Non-Coding RNAs.
LF338274 - JP 2014500723-A/145777: Polycomb-Associated Non-Coding RNAs.
LF329894 - JP 2014500723-A/137397: Polycomb-Associated Non-Coding RNAs.
JD323279 - Sequence 304303 from Patent EP1572962.
JD099986 - Sequence 81010 from Patent EP1572962.
JD323413 - Sequence 304437 from Patent EP1572962.
MA565446 - JP 2018138019-A/137372: Polycomb-Associated Non-Coding RNAs.
MA565447 - JP 2018138019-A/137373: Polycomb-Associated Non-Coding RNAs.
MA565460 - JP 2018138019-A/137386: Polycomb-Associated Non-Coding RNAs.
MA565471 - JP 2018138019-A/137397: Polycomb-Associated Non-Coding RNAs.
MA446071 - JP 2018138019-A/17997: Polycomb-Associated Non-Coding RNAs.
MA573852 - JP 2018138019-A/145778: Polycomb-Associated Non-Coding RNAs.
MA573851 - JP 2018138019-A/145777: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001202547, NP_001189476, OMP25, P57105, Q49SH3, Q96IA4, SYJ2B_HUMAN, SYNJ2BP
UCSC ID: uc021rvn.1
RefSeq Accession: NM_001202547
Protein: P57105 (aka SYJ2B_HUMAN or SJ2B_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001202547.2
exon count: 6CDS single in 3' UTR: no RNA size: 1955
ORF size: 576CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1352.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.