T03F1.9 | HoloCentric chromosome binding Protein 4

The hcp-4 gene encodes a centromere protein (CENP)-C homolog, holocentric protein (HCP)-4.

Graphics for hcp-4

3'UTR Zoom

see this gene in GBrowse
Legend: Blue:ORF, Gray:Updated 3'UTRome V3 dataset.

Operon Information

This gene is part of the operon CEOP1120 (I:3865940..3854185)
CEOP1120 contains 4 genes in the following order:
Blumenthal et al., Nature 417, 851-854
Click the picture below to launch Gbrowse

3'UTR mapped for hcp-4

If available, we display here the 3'UTRs sequences we obtained by our analysis (in FASTA format). Putative canonical PAS sites, if found, are highlighted in yellow.

1 ID: 1779 - Tier: 1 - Name: hcp-4 - Cosmid: T03F1.9 - WBGeneID: WBGene00001832 - Length: 104 - PAS: AATAAA
Cluster Coverage (%): 2167 reads (100.00%)
(See this 3'UTR in GBrowse!) (See this Gene in GBrowse!)

id Name Chr Strand Start End Length PAS Coverage
1779 hcp-4 I - 3862833 3862935 104nt AATAAA (-20nt) 2167 reads

This 3'UTR isoform has been detected in the following tissues:
UTRome v31 Intestine2 Pharynx2 Body Muscle2 Arcade cells2 GABA neurons2 NMDA neurons2 Hypodermis2 Seam cells2
1Murari et al., 2023
2Blazie et al., 2016 - Alternative polyadenylation directs tissue specific miRNA targeting in Caenorhabditis elegans somatic tissues. - under review (mixed stages & tissue-specific datasets)
agaaauaacuauugcuccacuauuuagcaaugucaaaaaacccaucuaaucccaauaccuguaaauaaugcaauuuuaaa gggaauaaaguuugaaucuguca

Updated miRanda Targets for hcp-4 (Murari et al., submitted)

hcp-4 transcript has been predicted to be targeted by the following miRNAs:

ID miRNA Target Gene Score Energy % Binding (Target) % Binding (miRNA)
110812 cel-miR-4927 hcp-4 164 -12.68 73.68 78.95

Predicted or Experimental Interactors for hcp-4 (WormBase)

hcp-4 has been predicted to interact with the following genes (data from WS200):

  • cul-2 Lee I et al. (2008)
    cul-2 encodes an E3 ubiquitin ligase; during development, CUL-2 functions as part of a Cul2-RING ubiquitin-ligase complex that regulates diverse biological processes, such as the initiation of meiotic anaphase II, cytokinesis and mitotic chromosome segregation, embryonic cell fate specification, and sex determination, via ubiquitin-mediated proteolysis; targets of CUL-2-mediated degradation include CYB-1/cyclin B and the zinc-finger protein TRA-1; CUL-2 is expressed in diverse cell types during embryonic and larval development and is also expressed in the adult germ line.
  • elpc-3 Lee I et al. (2008)
    none available
  • glh-1 Lee I et al. (2008)
    glh-1 encodes a putative DEAD-box RNA helicase that contains four CCHC zinc fingers and is homologous to Drosophila VASA, a germ-line-specific, ATP-dependent RNA helicase; at permissive temperature, GLH-1 is required redundantly with GLH-4 for proper germ-line development and fertility, specifically for regulating the normal extent of germ-line proliferation, oogenesis, and the production of functional sperm; GLH-1 activity is also likely required for the wild-type morphology of P granules and for localization of several protein components, such as PGL-1, but not for accumulation of P granule mRNAs; GLH-1 interacts in vivo with CSN-5, a COP9 signalosome component, and in vitro with itself and with KGB-1, a JNK-like MAP kinase, ZYX-1, a LIM domain-containing zyxin homologue, and GLH-3; GLH-1 is a constitutive P granule component and thus, with the exception of mature sperm, is expressed in germ cells at all stages of development; consistent with its P granule localization, GLH-1 is cytoplasmic in oocytes and the early embryo, while perinuclear in all later developmental stages as well as in the distal and medial regions of the hermaphrodite gonad; GLH-1 is also expressed in males.
  • hcp-1 Lee I et al. (2008)
    hcp-1 encodes a homolog of the mammalian centromere protein-F (CENP-F) and is involved in mitotic chromosome segregation; hcp-1 functions in an ordered pathway consisting of two other CENP proteins encoded by hcp-3 and hcp-4 to control assembly of the kinetochore; hcp-1 localization to the kinetochore is dependent on hcp-3 and hcp-4.
  • lst-3 Lee I et al. (2008)
    none available
  • mis-12 Zhong W et al. (2006)
    mis-12 encodes the C. elegans homolog of human and Schizosaccharomyces pombe Mis12 protein; mis-12 activity is required for proper attachment of chromosomes to the mitotic spindle and thus, for embryonic development; MIS-12 localizes to the kinetochore throughout mitosis, and this localization requires the activity of KNL-3, a novel kinetochore component with which MIS-12 co-purifies as part of a large complex of interacting kinetochore proteins.
  • nos-3 Lee I et al. (2008)
    nos-3 encodes a homolog of Drosophila NANOS that physically interacts with FBF-1 (similar, though not orthologous, to Drosophila PUMILIO); NOS-3 is required in development of the hermaphrodite germ-line to promote the switch from sperm to oocyte production, perhaps by forming a complex with FBF-1 that controls fem-3 mRNA.
  • vps-39 Lee I et al. (2008)


© The Biodesign Institute at Arizona State University - PO Box 875001, Tempe, AZ 85287-5001