Human Gene SHLD2 (ENST00000298784.5_6) from GENCODE V47lift37
  Description: shieldin complex subunit 2, transcript variant 18 (from RefSeq NR_165105.1)
Gencode Transcript: ENST00000298784.5_6
Gencode Gene: ENSG00000122376.12_12
Transcript (Including UTRs)
   Position: hg19 chr10:88,854,953-88,951,220 Size: 96,268 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr10:88,911,112-88,950,440 Size: 39,329 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:88,854,953-88,951,220)mRNA (may differ from genome)Protein (835 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FA35A_HUMAN
DESCRIPTION: RecName: Full=Protein FAM35A;
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the FAM35 family.

-  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


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.05 RPKM in Thyroid
Total median expression: 352.84 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -34.40114-0.302 Picture PostScript Text
3' UTR -196.30780-0.252 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
  Pfam Domains:
PF15793 - Protein family FAM35, C-terminal

SCOP Domains:
50249 - Nucleic acid-binding proteins

ModBase Predicted Comparative 3D Structure on Q86V20
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Descriptions from all associated GenBank mRNAs
  AK022978 - Homo sapiens cDNA FLJ12916 fis, clone NT2RP2004551.
LF384977 - JP 2014500723-A/192480: Polycomb-Associated Non-Coding RNAs.
BC051863 - Homo sapiens family with sequence similarity 35, member A, mRNA (cDNA clone MGC:60227 IMAGE:6146593), complete cds.
MA620554 - JP 2018138019-A/192480: Polycomb-Associated Non-Coding RNAs.
CU690872 - Synthetic construct Homo sapiens gateway clone IMAGE:100021520 5' read FAM35A mRNA.
KJ894037 - Synthetic construct Homo sapiens clone ccsbBroadEn_03431 FAM35A gene, encodes complete protein.
JD263951 - Sequence 244975 from Patent EP1572962.
JD303102 - Sequence 284126 from Patent EP1572962.
LF333888 - JP 2014500723-A/141391: Polycomb-Associated Non-Coding RNAs.
JD327425 - Sequence 308449 from Patent EP1572962.
JD050147 - Sequence 31171 from Patent EP1572962.
LF333887 - JP 2014500723-A/141390: Polycomb-Associated Non-Coding RNAs.
JD502375 - Sequence 483399 from Patent EP1572962.
AK025606 - Homo sapiens cDNA: FLJ21953 fis, clone HEP05120, highly similar to AF131775 Homo sapiens clone 25033 mRNA sequence.
JD141383 - Sequence 122407 from Patent EP1572962.
JD344944 - Sequence 325968 from Patent EP1572962.
JD300379 - Sequence 281403 from Patent EP1572962.
JD093400 - Sequence 74424 from Patent EP1572962.
AF131775 - Homo sapiens clone 25033 mRNA sequence, partial cds.
AK025471 - Homo sapiens cDNA: FLJ21818 fis, clone HEP01165, highly similar to AF131775 Homo sapiens clone 25033 mRNA sequence.
JD107002 - Sequence 88026 from Patent EP1572962.
JD499386 - Sequence 480410 from Patent EP1572962.
JD241093 - Sequence 222117 from Patent EP1572962.
MA569465 - JP 2018138019-A/141391: Polycomb-Associated Non-Coding RNAs.
MA569464 - JP 2018138019-A/141390: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000298784.1, ENST00000298784.2, ENST00000298784.3, ENST00000298784.4, FAM35A , NR_165105, O95885, Q86V20, Q9H991, RINN2 , SHLD2 , SHLD2_HUMAN, uc317mgb.1, uc317mgb.2
UCSC ID: ENST00000298784.5_6
RefSeq Accession: NM_019054.3
Protein: Q86V20 (aka FA35A_HUMAN)

-  Gene Model Information
  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.