Human Gene NXNL1 (ENST00000301944.3) from GENCODE V44
  Description: Homo sapiens nucleoredoxin like 1 (NXNL1), mRNA. (from RefSeq NM_138454)
RefSeq Summary (NM_138454): Retinitis pigmentosa (RP) is a disease that leads to blindness by degeneration of cone photoreceptors. Rods produce factors required for cone viability. The protein encoded by this gene is one of those factors and is similar to a truncated form of thioredoxin. This gene has been proposed to have therapeutic value against RP. [provided by RefSeq, Dec 2015].
Gencode Transcript: ENST00000301944.3
Gencode Gene: ENSG00000171773.3
Transcript (Including UTRs)
   Position: hg38 chr19:17,455,425-17,460,926 Size: 5,502 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr19:17,455,647-17,460,869 Size: 5,223 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:17,455,425-17,460,926)mRNA (may differ from genome)Protein (212 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NXNL1_HUMAN
DESCRIPTION: RecName: Full=Nucleoredoxin-like protein 1; AltName: Full=Thioredoxin-like protein 6;
FUNCTION: May play a role in cone cell viability, slowing down cone degeneration, does not seem to play a role in degenerating rods (By similarity).
SUBCELLULAR LOCATION: Nucleus outer membrane (By similarity).
SIMILARITY: Belongs to the nucleoredoxin family.
SIMILARITY: Contains 1 thioredoxin domain.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: NXNL1
Diseases sorted by gene-association score: retinitis pigmentosa (3), bardet-biedl syndrome (2), leber congenital amaurosis (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.4057-0.218 Picture PostScript Text
3' UTR -90.50222-0.408 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
IPR012336 - Thioredoxin-like_fold

ModBase Predicted Comparative 3D Structure on Q96CM4
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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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004791 thioredoxin-disulfide reductase activity

Biological Process:
GO:0045454 cell redox homeostasis
GO:0045494 photoreceptor cell maintenance
GO:0098869 cellular oxidant detoxification

Cellular Component:
GO:0005634 nucleus
GO:0005640 nuclear outer membrane
GO:0005737 cytoplasm
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  JD135727 - Sequence 116751 from Patent EP1572962.
BC014127 - Homo sapiens nucleoredoxin-like 1, mRNA (cDNA clone MGC:20742 IMAGE:4579939), complete cds.
JD551544 - Sequence 532568 from Patent EP1572962.
JD350716 - Sequence 331740 from Patent EP1572962.
JD523787 - Sequence 504811 from Patent EP1572962.
JD246905 - Sequence 227929 from Patent EP1572962.
JD452274 - Sequence 433298 from Patent EP1572962.
JD246906 - Sequence 227930 from Patent EP1572962.
JD139905 - Sequence 120929 from Patent EP1572962.
JD246904 - Sequence 227928 from Patent EP1572962.
JD413378 - Sequence 394402 from Patent EP1572962.
JD128394 - Sequence 109418 from Patent EP1572962.
JD212697 - Sequence 193721 from Patent EP1572962.
JD391794 - Sequence 372818 from Patent EP1572962.
JD389781 - Sequence 370805 from Patent EP1572962.
JD121701 - Sequence 102725 from Patent EP1572962.
JD448945 - Sequence 429969 from Patent EP1572962.
JD219152 - Sequence 200176 from Patent EP1572962.
HQ448672 - Synthetic construct Homo sapiens clone IMAGE:100072114; CCSB007350_02 thioredoxin-like 6 (NXNL1) gene, encodes complete protein.
KJ900030 - Synthetic construct Homo sapiens clone ccsbBroadEn_09424 NXNL1 gene, encodes complete protein.
DQ426894 - Homo sapiens thioredoxin-like 6 (TXNL6) mRNA, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000301944.1, ENST00000301944.2, NM_138454, NXNL1_HUMAN, Q96CM4, TXNL6, uc002ngs.1, uc002ngs.2, uc002ngs.3, uc002ngs.4, uc002ngs.5
UCSC ID: ENST00000301944.3
RefSeq Accession: NM_138454
Protein: Q96CM4 (aka NXNL1_HUMAN)
CCDS: CCDS12360.1

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