Human Gene LARP1 (ENST00000518297.6_10) from GENCODE V47lift37
  Description: La ribonucleoprotein 1, translational regulator, transcript variant 2 (from RefSeq NM_033551.3)
Gencode Transcript: ENST00000518297.6_10
Gencode Gene: ENSG00000155506.19_16
Transcript (Including UTRs)
   Position: hg19 chr5:154,134,937-154,197,165 Size: 62,229 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr5:154,135,318-154,193,656 Size: 58,339 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:154,134,937-154,197,165)mRNA (may differ from genome)Protein (1096 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LARP1_HUMAN
DESCRIPTION: RecName: Full=La-related protein 1; AltName: Full=La ribonucleoprotein domain family member 1;
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the LARP family.
SIMILARITY: Contains 1 HTH La-type RNA-binding domain.
SEQUENCE CAUTION: Sequence=AAH33856.1; Type=Erroneous initiation; Sequence=BAA34451.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;

-  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

+  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: 39.66 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1209.84 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 -217.20381-0.570 Picture PostScript Text
3' UTR -1206.193509-0.344 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
IPR006607 - DM15
IPR006630 - Lupus_La_RNA-bd
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF05383 - La domain

SCOP Domains:
46785 - "Winged helix" DNA-binding domain
52080 - Ribosomal proteins L15p and L18e
63411 - LuxS/MPP-like metallohydrolase

ModBase Predicted Comparative 3D Structure on Q6PKG0
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 orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000339 RNA cap binding
GO:0003723 RNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0005515 protein binding
GO:0008190 eukaryotic initiation factor 4E binding
GO:0008494 translation activator activity
GO:0031369 translation initiation factor binding
GO:0045296 cadherin binding
GO:0048027 mRNA 5'-UTR binding

Biological Process:
GO:0006412 translation
GO:0006413 translational initiation
GO:0006417 regulation of translation
GO:0008283 cell proliferation
GO:0016239 positive regulation of macroautophagy
GO:0017148 negative regulation of translation
GO:0031929 TOR signaling
GO:0038202 TORC1 signaling
GO:0045070 positive regulation of viral genome replication
GO:0045727 positive regulation of translation
GO:0048255 mRNA stabilization
GO:0072752 cellular response to rapamycin
GO:1990928 response to amino acid starvation

Cellular Component:
GO:0005737 cytoplasm
GO:0010494 cytoplasmic stress granule
GO:0016020 membrane
GO:0005844 polysome
GO:0031931 TORC1 complex


-  Descriptions from all associated GenBank mRNAs
  BC001460 - Homo sapiens La ribonucleoprotein domain family, member 1, mRNA (cDNA clone MGC:2954 IMAGE:3138935), complete cds.
CU674716 - Synthetic construct Homo sapiens gateway clone IMAGE:100020575 5' read LARP1 mRNA.
JF432319 - Synthetic construct Homo sapiens clone IMAGE:100073505 La ribonucleoprotein domain family, member 1 (LARP1) gene, encodes complete protein.
KJ898477 - Synthetic construct Homo sapiens clone ccsbBroadEn_07871 LARP1 gene, encodes complete protein.
AB018274 - Homo sapiens mRNA for KIAA0731 protein, partial cds.
AK091465 - Homo sapiens cDNA FLJ34146 fis, clone FCBBF3011889, weakly similar to Drosophila melanogaster La related protein (larp) mRNA.
AX747001 - Sequence 526 from Patent EP1308459.
AK307554 - Homo sapiens cDNA, FLJ97502.
JD369201 - Sequence 350225 from Patent EP1572962.
JD133626 - Sequence 114650 from Patent EP1572962.
JD154772 - Sequence 135796 from Patent EP1572962.
JD168704 - Sequence 149728 from Patent EP1572962.
JD371006 - Sequence 352030 from Patent EP1572962.
JD461021 - Sequence 442045 from Patent EP1572962.
JD044734 - Sequence 25758 from Patent EP1572962.
JD044009 - Sequence 25033 from Patent EP1572962.
JD104965 - Sequence 85989 from Patent EP1572962.
JD069487 - Sequence 50511 from Patent EP1572962.
JD269425 - Sequence 250449 from Patent EP1572962.
JD203217 - Sequence 184241 from Patent EP1572962.
JD250744 - Sequence 231768 from Patent EP1572962.
JD167749 - Sequence 148773 from Patent EP1572962.
JD099209 - Sequence 80233 from Patent EP1572962.
JD363192 - Sequence 344216 from Patent EP1572962.
JD361081 - Sequence 342105 from Patent EP1572962.
JD478362 - Sequence 459386 from Patent EP1572962.
JD370387 - Sequence 351411 from Patent EP1572962.
JD128210 - Sequence 109234 from Patent EP1572962.
JD142305 - Sequence 123329 from Patent EP1572962.
JD257890 - Sequence 238914 from Patent EP1572962.
JD471128 - Sequence 452152 from Patent EP1572962.
JD164547 - Sequence 145571 from Patent EP1572962.
JD401321 - Sequence 382345 from Patent EP1572962.
JD078548 - Sequence 59572 from Patent EP1572962.
AL133034 - Homo sapiens mRNA; cDNA DKFZp727K171 (from clone DKFZp727K171).
JD320617 - Sequence 301641 from Patent EP1572962.
JD161958 - Sequence 142982 from Patent EP1572962.
JD383891 - Sequence 364915 from Patent EP1572962.
JD492431 - Sequence 473455 from Patent EP1572962.
JD387236 - Sequence 368260 from Patent EP1572962.
JD141263 - Sequence 122287 from Patent EP1572962.
JD250572 - Sequence 231596 from Patent EP1572962.
JD421122 - Sequence 402146 from Patent EP1572962.
JD259062 - Sequence 240086 from Patent EP1572962.
JD411427 - Sequence 392451 from Patent EP1572962.
BC033856 - Homo sapiens La ribonucleoprotein domain family, member 1, mRNA (cDNA clone IMAGE:5123380), complete cds.
JD125147 - Sequence 106171 from Patent EP1572962.
KJ904686 - Synthetic construct Homo sapiens clone ccsbBroadEn_14080 LARP1 gene, encodes complete protein.
JD113810 - Sequence 94834 from Patent EP1572962.
EU446783 - Synthetic construct Homo sapiens clone IMAGE:100070104; IMAGE:100011992; FLH257408.01L La ribonucleoprotein domain family, member 1 (LARP1) gene, encodes complete protein.
JD286097 - Sequence 267121 from Patent EP1572962.
JD258257 - Sequence 239281 from Patent EP1572962.
JD336243 - Sequence 317267 from Patent EP1572962.
JD110813 - Sequence 91837 from Patent EP1572962.
JD086921 - Sequence 67945 from Patent EP1572962.
JD324952 - Sequence 305976 from Patent EP1572962.
JD123648 - Sequence 104672 from Patent EP1572962.
BC038220 - Homo sapiens La ribonucleoprotein domain family, member 1, mRNA (cDNA clone IMAGE:4099180).
AK057839 - Homo sapiens cDNA FLJ25110 fis, clone CBR01680.
JD214479 - Sequence 195503 from Patent EP1572962.
BC010144 - Homo sapiens La ribonucleoprotein domain family, member 1, mRNA (cDNA clone IMAGE:4304831).
JD116410 - Sequence 97434 from Patent EP1572962.
JD164782 - Sequence 145806 from Patent EP1572962.
JD259610 - Sequence 240634 from Patent EP1572962.
DQ593218 - Homo sapiens piRNA piR-33330, complete sequence.
JD424510 - Sequence 405534 from Patent EP1572962.
JD268974 - Sequence 249998 from Patent EP1572962.
JD227001 - Sequence 208025 from Patent EP1572962.
JD372118 - Sequence 353142 from Patent EP1572962.
JD488629 - Sequence 469653 from Patent EP1572962.
JD290301 - Sequence 271325 from Patent EP1572962.
BC015573 - Homo sapiens La ribonucleoprotein domain family, member 1, mRNA (cDNA clone IMAGE:3837786), with apparent retained intron.
JD439723 - Sequence 420747 from Patent EP1572962.
JD055046 - Sequence 36070 from Patent EP1572962.
BC003063 - Homo sapiens cDNA clone IMAGE:3506392.
JD157017 - Sequence 138041 from Patent EP1572962.
JD147897 - Sequence 128921 from Patent EP1572962.
JD185066 - Sequence 166090 from Patent EP1572962.
JD467778 - Sequence 448802 from Patent EP1572962.
JD441307 - Sequence 422331 from Patent EP1572962.
JD457867 - Sequence 438891 from Patent EP1572962.
JD271009 - Sequence 252033 from Patent EP1572962.
JD486796 - Sequence 467820 from Patent EP1572962.
JD214548 - Sequence 195572 from Patent EP1572962.
JD394590 - Sequence 375614 from Patent EP1572962.
JD394118 - Sequence 375142 from Patent EP1572962.
JD506369 - Sequence 487393 from Patent EP1572962.
JD160583 - Sequence 141607 from Patent EP1572962.
JD419668 - Sequence 400692 from Patent EP1572962.
JD356072 - Sequence 337096 from Patent EP1572962.
JD145697 - Sequence 126721 from Patent EP1572962.
JD081673 - Sequence 62697 from Patent EP1572962.
JD483373 - Sequence 464397 from Patent EP1572962.
JD249243 - Sequence 230267 from Patent EP1572962.
AK312203 - Homo sapiens cDNA, FLJ92492.
KJ906087 - Synthetic construct Homo sapiens clone ccsbBroadEn_15757 LARP1 gene, encodes complete protein.
JD503712 - Sequence 484736 from Patent EP1572962.
JD103127 - Sequence 84151 from Patent EP1572962.
JD374697 - Sequence 355721 from Patent EP1572962.
JD455948 - Sequence 436972 from Patent EP1572962.
JD123705 - Sequence 104729 from Patent EP1572962.
JD551427 - Sequence 532451 from Patent EP1572962.
JD300034 - Sequence 281058 from Patent EP1572962.
JD539391 - Sequence 520415 from Patent EP1572962.
JD469125 - Sequence 450149 from Patent EP1572962.
JD526702 - Sequence 507726 from Patent EP1572962.
JD130040 - Sequence 111064 from Patent EP1572962.
JD050973 - Sequence 31997 from Patent EP1572962.
JD276619 - Sequence 257643 from Patent EP1572962.
JD297461 - Sequence 278485 from Patent EP1572962.
JD357777 - Sequence 338801 from Patent EP1572962.
JD357775 - Sequence 338799 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000518297.1, ENST00000518297.2, ENST00000518297.3, ENST00000518297.4, ENST00000518297.5, KIAA0731, LARP, LARP1_HUMAN, NM_033551, O94836, Q6PKG0, Q8N4M2, Q8NB73, Q9UFD7, uc323qrt.1, uc323qrt.2
UCSC ID: ENST00000518297.6_10
RefSeq Accession: NM_033551.3
Protein: Q6PKG0 (aka LARP1_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.