Human Gene CARNMT1 (ENST00000376834.8) from GENCODE V44
  Description: Homo sapiens carnosine N-methyltransferase 1 (CARNMT1), transcript variant 3, non-coding RNA. (from RefSeq NR_135282)
RefSeq Summary (NM_152420): The protein encoded by this gene is a methyltransferase that converts carnosine to anserine, a dipeptide found abundantly in skeletal muscle. The encoded protein can methylate other dipeptides as well. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2016].
Gencode Transcript: ENST00000376834.8
Gencode Gene: ENSG00000156017.13
Transcript (Including UTRs)
   Position: hg38 chr9:74,980,790-75,028,293 Size: 47,504 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg38 chr9:74,983,767-75,028,241 Size: 44,475 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:74,980,790-75,028,293)mRNA (may differ from genome)Protein (409 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHPRD
LynxMalacardsMGImyGene2neXtProtOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CI041_HUMAN
DESCRIPTION: RecName: Full=UPF0586 protein C9orf41;
SIMILARITY: Belongs to the UPF0586 family.
SEQUENCE CAUTION: Sequence=BAC05369.1; 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


-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.08 RPKM in Testis
Total median expression: 154.92 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 -21.2052-0.408 Picture PostScript Text
3' UTR -657.202977-0.221 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
IPR012901 - N2227

Pfam Domains:
PF07942 - N2227-like protein

ModBase Predicted Comparative 3D Structure on Q8N4J0
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-  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 BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGIRGDEnsemblEnsemblWormBaseSGD
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
AlignmentAlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0030735 carnosine N-methyltransferase activity

Biological Process:
GO:0006548 histidine catabolic process
GO:0032259 methylation
GO:0035498 carnosine metabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF211275 - JP 2014500723-A/18778: Polycomb-Associated Non-Coding RNAs.
MA446852 - JP 2018138019-A/18778: Polycomb-Associated Non-Coding RNAs.
BX647386 - Homo sapiens mRNA; cDNA DKFZp686C13144 (from clone DKFZp686C13144).
BX538061 - Homo sapiens mRNA; cDNA DKFZp686J16172 (from clone DKFZp686J16172).
LF208560 - JP 2014500723-A/16063: Polycomb-Associated Non-Coding RNAs.
MA444137 - JP 2018138019-A/16063: Polycomb-Associated Non-Coding RNAs.
LF377868 - JP 2014500723-A/185371: Polycomb-Associated Non-Coding RNAs.
MA613445 - JP 2018138019-A/185371: Polycomb-Associated Non-Coding RNAs.
LF377869 - JP 2014500723-A/185372: Polycomb-Associated Non-Coding RNAs.
MA613446 - JP 2018138019-A/185372: Polycomb-Associated Non-Coding RNAs.
LF345149 - JP 2014500723-A/152652: Polycomb-Associated Non-Coding RNAs.
MA580726 - JP 2018138019-A/152652: Polycomb-Associated Non-Coding RNAs.
LF209816 - JP 2014500723-A/17319: Polycomb-Associated Non-Coding RNAs.
MA445393 - JP 2018138019-A/17319: Polycomb-Associated Non-Coding RNAs.
BC034033 - Homo sapiens chromosome 9 open reading frame 41, mRNA (cDNA clone MGC:24721 IMAGE:4278547), complete cds.
JD089816 - Sequence 70840 from Patent EP1572962.
JD188071 - Sequence 169095 from Patent EP1572962.
JD398631 - Sequence 379655 from Patent EP1572962.
JD070427 - Sequence 51451 from Patent EP1572962.
JD071321 - Sequence 52345 from Patent EP1572962.
JD555790 - Sequence 536814 from Patent EP1572962.
JD203884 - Sequence 184908 from Patent EP1572962.
JD160201 - Sequence 141225 from Patent EP1572962.
JD245770 - Sequence 226794 from Patent EP1572962.
JD337762 - Sequence 318786 from Patent EP1572962.
JD337763 - Sequence 318787 from Patent EP1572962.
JD248835 - Sequence 229859 from Patent EP1572962.
JD084935 - Sequence 65959 from Patent EP1572962.
JD463327 - Sequence 444351 from Patent EP1572962.
JD337761 - Sequence 318785 from Patent EP1572962.
JD161816 - Sequence 142840 from Patent EP1572962.
JD153370 - Sequence 134394 from Patent EP1572962.
JD198515 - Sequence 179539 from Patent EP1572962.
JD140654 - Sequence 121678 from Patent EP1572962.
JD321207 - Sequence 302231 from Patent EP1572962.
JD321208 - Sequence 302232 from Patent EP1572962.
JD388641 - Sequence 369665 from Patent EP1572962.
JD123866 - Sequence 104890 from Patent EP1572962.
JD253099 - Sequence 234123 from Patent EP1572962.
JD388640 - Sequence 369664 from Patent EP1572962.
JD388642 - Sequence 369666 from Patent EP1572962.
JD252492 - Sequence 233516 from Patent EP1572962.
JD415596 - Sequence 396620 from Patent EP1572962.
JD228408 - Sequence 209432 from Patent EP1572962.
JD525353 - Sequence 506377 from Patent EP1572962.
JD547949 - Sequence 528973 from Patent EP1572962.
JD547948 - Sequence 528972 from Patent EP1572962.
JD161815 - Sequence 142839 from Patent EP1572962.
JD327799 - Sequence 308823 from Patent EP1572962.
AK098661 - Homo sapiens cDNA FLJ25795 fis, clone TST07031.
JD056683 - Sequence 37707 from Patent EP1572962.
JD412145 - Sequence 393169 from Patent EP1572962.
HQ447650 - Synthetic construct Homo sapiens clone IMAGE:100070996; CCSB012841_02 chromosome 9 open reading frame 41 (C9orf41) gene, encodes complete protein.
KJ895522 - Synthetic construct Homo sapiens clone ccsbBroadEn_04916 C9orf41 gene, encodes complete protein.
EU832520 - Synthetic construct Homo sapiens clone HAIB:100067549; DKFZo008H0629 chromosome 9 open reading frame 41 protein (C9orf41) gene, encodes complete protein.
EU832602 - Synthetic construct Homo sapiens clone HAIB:100067631; DKFZo004H0630 chromosome 9 open reading frame 41 protein (C9orf41) gene, encodes complete protein.
AK299691 - Homo sapiens cDNA FLJ58856 complete cds.
LF377870 - JP 2014500723-A/185373: Polycomb-Associated Non-Coding RNAs.
MA613447 - JP 2018138019-A/185373: Polycomb-Associated Non-Coding RNAs.
LF331855 - JP 2014500723-A/139358: Polycomb-Associated Non-Coding RNAs.
MA567432 - JP 2018138019-A/139358: Polycomb-Associated Non-Coding RNAs.
LF377871 - JP 2014500723-A/185374: Polycomb-Associated Non-Coding RNAs.
MA613448 - JP 2018138019-A/185374: Polycomb-Associated Non-Coding RNAs.
LF331854 - JP 2014500723-A/139357: Polycomb-Associated Non-Coding RNAs.
MA567431 - JP 2018138019-A/139357: Polycomb-Associated Non-Coding RNAs.
LF377872 - JP 2014500723-A/185375: Polycomb-Associated Non-Coding RNAs.
MA613449 - JP 2018138019-A/185375: Polycomb-Associated Non-Coding RNAs.
LF331853 - JP 2014500723-A/139356: Polycomb-Associated Non-Coding RNAs.
MA567430 - JP 2018138019-A/139356: Polycomb-Associated Non-Coding RNAs.
CU689816 - Synthetic construct Homo sapiens gateway clone IMAGE:100022282 5' read C9orf41 mRNA.
LF377873 - JP 2014500723-A/185376: Polycomb-Associated Non-Coding RNAs.
MA613450 - JP 2018138019-A/185376: Polycomb-Associated Non-Coding RNAs.
LF331852 - JP 2014500723-A/139355: Polycomb-Associated Non-Coding RNAs.
MA567429 - JP 2018138019-A/139355: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8N4J0 (Reactome details) participates in the following event(s):

R-HSA-8876789 CARNMT1 methylates CARN to Anserine
R-HSA-70921 Histidine catabolism
R-HSA-6788656 Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: C9orf41, CI041_HUMAN, ENST00000376834.1, ENST00000376834.2, ENST00000376834.3, ENST00000376834.4, ENST00000376834.5, ENST00000376834.6, ENST00000376834.7, NR_135282, Q7Z383, Q8N4J0, Q8N7C5, uc004ajq.1, uc004ajq.2, uc004ajq.3, uc004ajq.4, uc004ajq.5
UCSC ID: ENST00000376834.8
RefSeq Accession: NM_152420
Protein: Q8N4J0 (aka CI041_HUMAN)
CCDS: CCDS6649.1

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