Human Gene CCL3L3 (uc002hlf.2)
  Description: Homo sapiens chemokine (C-C motif) ligand 3-like 1 (CCL3L3), mRNA.
RefSeq Summary (NM_021006): This gene is one of several cytokine genes that are clustered on the q-arm of chromosome 17. Cytokines are a family of secreted proteins that function in inflammatory and immunoregulatory processes. The protein encoded by this gene binds to several chemokine receptors, including chemokine binding protein 2 and chemokine (C-C motif) receptor 5 (CCR5). CCR5 is a co-receptor for HIV, and binding of this protein to CCR5 inhibits HIV entry. The copy number of this gene varies among individuals, where most individuals have one to six copies, and a minority of individuals have zero or more than six copies. There are conflicting reports about copy number variation of this gene and its correlation to disease susceptibility. This record represents one of two copies that are present on the ALT_REF_LOCI_2 alternate haplotype of the GRCh38 human reference genome assembly. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2014].
Transcript (Including UTRs)
   Position: hg19 chr17:34,522,268-34,524,156 Size: 1,889 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr17:34,522,685-34,524,072 Size: 1,388 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:34,522,268-34,524,156)mRNA (may differ from genome)Protein (93 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CL3L1_HUMAN
DESCRIPTION: RecName: Full=C-C motif chemokine 3-like 1; AltName: Full=G0/G1 switch regulatory protein 19-2; AltName: Full=LD78-beta(1-70); AltName: Full=PAT 464.2; AltName: Full=Small-inducible cytokine A3-like 1; AltName: Full=Tonsillar lymphocyte LD78 beta protein; Contains: RecName: Full=LD78-beta(3-70); Contains: RecName: Full=LD78-beta(5-70); Flags: Precursor;
FUNCTION: Chemotactic for lymphocytes and monocytes. Is a ligand for CCR1, CCR3 and CCR5. Is an inhibitor of HIV-1-infection. The processed form LD78-beta(3-70) shows a 20-fold to 30-fold higher chemotactic activity and is a very potent inhibitor of HIV-1- infection. LD78-beta(3-70) is also a ligand for CCR1, CCR3 and CCR5.
SUBCELLULAR LOCATION: Secreted.
PTM: The N-terminal processed forms LD78-beta(3-70) and LD78- beta(5-70) are produced by proteolytic cleavage after secretion from peripheral blood monocytes. The cleavage to yield LD78- beta(3-70) is probably achieved by DPP4.
POLYMORPHISM: The copy number of the CCL3L1 gene varies among individuals; most individuals have 1-6 copies in the diploid genome, although rare individuals have zero or more than 6 copies.
SIMILARITY: Belongs to the intercrine beta (chemokine CC) family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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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
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -24.1684-0.288 Picture PostScript Text
3' UTR -129.60417-0.311 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
IPR000827 - Chemokine_CC_CS
IPR001811 - Chemokine_IL8-like_dom

Pfam Domains:
PF00048 - Small cytokines (intecrine/chemokine), interleukin-8 like

SCOP Domains:
54117 - Interleukin 8-like chemokines

ModBase Predicted Comparative 3D Structure on P16619
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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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0008009 chemokine activity
GO:0048020 CCR chemokine receptor binding

Biological Process:
GO:0002548 monocyte chemotaxis
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007186 G-protein coupled receptor signaling pathway
GO:0008285 negative regulation of cell proliferation
GO:0010469 regulation of receptor activity
GO:0019221 cytokine-mediated signaling pathway
GO:0030593 neutrophil chemotaxis
GO:0043547 positive regulation of GTPase activity
GO:0048247 lymphocyte chemotaxis
GO:0070098 chemokine-mediated signaling pathway
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071346 cellular response to interferon-gamma
GO:0071347 cellular response to interleukin-1
GO:0071356 cellular response to tumor necrosis factor

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  BC007783 - Homo sapiens chemokine (C-C motif) ligand 3-like 3, mRNA (cDNA clone MGC:12815 IMAGE:4308472), complete cds.
BC027888 - Homo sapiens chemokine (C-C motif) ligand 3-like 1, mRNA (cDNA clone MGC:34553 IMAGE:5222247), complete cds.
BC063472 - Homo sapiens chemokine (C-C motif) ligand 3-like 3, mRNA (cDNA clone IMAGE:5207922), with apparent retained intron.
X52149 - Human 464.2 mRNA for a cytokine effector of inflammatory response.
BC107710 - Homo sapiens chemokine (C-C motif) ligand 3-like 1, mRNA (cDNA clone MGC:104178 IMAGE:6699133), complete cds.
JD306609 - Sequence 287633 from Patent EP1572962.
JD331334 - Sequence 312358 from Patent EP1572962.
BC146914 - Homo sapiens chemokine (C-C motif) ligand 3-like 3, mRNA (cDNA clone MGC:182017 IMAGE:9056842), complete cds.
BC146919 - Homo sapiens chemokine (C-C motif) ligand 3-like 3, mRNA (cDNA clone MGC:182022 IMAGE:9056847), complete cds.
BC147008 - Homo sapiens chemokine (C-C motif) ligand 3-like 3, mRNA (cDNA clone MGC:182111 IMAGE:9056936), complete cds.
BC147013 - Homo sapiens chemokine (C-C motif) ligand 3-like 3, mRNA (cDNA clone MGC:182116 IMAGE:9056941), complete cds.
JD210097 - Sequence 191121 from Patent EP1572962.
JD216426 - Sequence 197450 from Patent EP1572962.
E03131 - cDNA encoding human peptide LD78 beta.
JD102727 - Sequence 83751 from Patent EP1572962.
JD338622 - Sequence 319646 from Patent EP1572962.
JD130583 - Sequence 111607 from Patent EP1572962.
JD400565 - Sequence 381589 from Patent EP1572962.
KJ892102 - Synthetic construct Homo sapiens clone ccsbBroadEn_01496 CCL3L1 gene, encodes complete protein.
KJ900753 - Synthetic construct Homo sapiens clone ccsbBroadEn_10147 CCL3L3 gene, encodes complete protein.
KJ892103 - Synthetic construct Homo sapiens clone ccsbBroadEn_01497 CCL3L1 gene, encodes complete protein.
BT006783 - Homo sapiens chemokine (C-C motif) ligand 3 mRNA, complete cds.
D63785 - Homo sapiens mRNA for LD78 alpha beta, partial cds.
JD423582 - Sequence 404606 from Patent EP1572962.
JD322684 - Sequence 303708 from Patent EP1572962.
JD167198 - Sequence 148222 from Patent EP1572962.
JD402872 - Sequence 383896 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04062 - Chemokine signaling pathway
hsa05142 - Chagas disease

Reactome (by CSHL, EBI, and GO)

Protein P16619 (Reactome details) participates in the following event(s):

R-HSA-6783783 Interleukin-10 signaling
R-HSA-449147 Signaling by Interleukins
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A6NGK6, B2RUX4, CCL3L1, CL3L1_HUMAN, D17S1718, G0S19-2, NM_021006, NP_066286, P16619, Q3B7A8, Q53YA5, Q96I68, SCYA3L1
UCSC ID: uc002hlf.2
RefSeq Accession: NM_021006
Protein: P16619 (aka CL3L1_HUMAN)
CCDS: CCDS32626.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_021006.4
exon count: 3CDS single in 3' UTR: no RNA size: 804
ORF size: 282CDS single in intron: no Alignment % ID: 99.87
txCdsPredict score: 761.00frame shift in genome: no % Coverage: 97.39
has start codon: yes stop codon in genome: no # of Alignments: 2
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.