| JCEG ID |
JCEG166 |
| Name |
sqv-6
WormBase
NCBI Gene
|
| Human Ortholog |
GGDB:XYLT1 XYLT2
OMIM:
608124
608125
OrthoList :
XYLT2
XYLT1
(Ensembl Compara)
GWAS Catalog
| STREAM | RAF | p-value | OR | BETA | CI | Study |
| DOWNSTREAM |
|
0.0000004
(Additive model)
|
2.5
|
|
[1.70-3.50] |
23478653
|
|
Han JY 2013-03-12 Pharmacogenomics J
A genome-wide association study of survival in small-cell lung cancer patients treated with irinotecan plus cisplatin chemotherapy.
|
| UPSTREAM |
0.09 |
0.000002
|
|
0.088
(unit decrease)
|
[NR] |
23322567
|
|
Lopes MC 2013-01-15 Invest Ophthalmol Vis Sci
Identification of a candidate gene for astigmatism.
|
| DOWNSTREAM |
0.015 |
0.0000008
(ALT )
|
|
0.04
(U/L increase)
|
[NR] |
23251661
|
|
Comuzzie AG 2012-12-04 PLoS One
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
|
| UPSTREAM |
0.006 |
0.000009
(ALT )
|
|
0.02
(U/L increase)
|
[NR] |
23251661
|
|
Comuzzie AG 2012-12-04 PLoS One
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
|
Option tblastn : Query Worm Protein, Subject GGDB mRNA, E-val < 0.00001
|
| Family Name |
XylT |
| Locus Tag |
Y50D4C.4
|
| RNAi phenotype |
|
phenotype
|
Emb (45% n=20, see reference)
|
|
Microscope observation (Image)
|
|
|
COPAS (Image)
|
Normal
|
|
hsp-4::GFP (Image)
|
|
|
| Sequence Features |
kr: soluble
|
| Sequence |
CDS
atgttattcaacgggacgactaaatatcgagattatgcgattgtgatatc
attattcttcctgctaaacgtctatttattgtacaatacggctcaacaca
cgcaagtcggaaattcgaagcatatttcgtcggatagcggtgaaaaaacg
tcgaatcctcttccatcatgcgaaatcacagatgacctggcgaaaagtgc
aatttcccgtgcaattactccatcctgcaaagcaaaactgcagctggaag
cttgtcaactgaaaaatgggacttttacaataaattttccggaaaatcaa
tgcccgaaccacgatagccggcttatcgaccaacgaatcggctgtttttt
ggacaaaaaagaggctcgagtgctcacagagttcgagtacaaacttccaa
agtcaaatgggaaagcgacgtgtcgaaagcactgctataaagctggtttt
ttgtatttcggacttgaattcggacacgaatgcttctgtgggaatgatgt
atcaaatgcgacggcggttgatgacgtggaatgtcgggcgtataaatgtc
cgggaaatgagaactcggaggagttctgtggtggattcaatgcagtcgag
atttttaggacaggatttagaagcaaagtgaatcaccgcaagccgacata
tcttccacctagcagcgattctatcaaaaatcccgtcaaaattctcttcc
ttcttcaattaaatggtagaaatgagcgtcaagtgaaacgatttctcaaa
tcaatttatcttccacatcattattactatatccacgtggatgcacgtca
gaattacatgttctcagaaatgcaaaaagttgctgattttctggataata
ttcatataaccgaacggagattcagcacaatttggggtggagcatcactt
ttacaaatgtttctgcaagtgattagggattcgatgaaaattgagaaatt
caaggattgggattatattattaatttctcggaaagtgatttcccgattc
taccgatttccgattttgagagacttatcactgtaaacaacggaaaatca
ttcctggcctcacacggctacaacactggaaaattcattcaaaaacaagg
attcgaatacgtgttctccgaatgcgataatcgaatgttccgtatcggaa
aacgcgaatttccacaaaatctacgaattgacggcggatccgattgggtt
ggaattcatcgaaatctcgccgaattttcgatttccgacgaggaattgcc
tcgaaaattgcgaaaaacgtatgaaagtatacttctaccactggaatcat
tctatcatactcttgcgttcaattccgaattctgtgatgatctactgatg
agcaatttgcggcttacgaattggtacaggaaacagggatgtcggtgtgc
ttcattgaagcctattgttgattggtgtggatgttcgccgctggtttttc
gtgaagaaactatgaagaaatttgagcttcaaaaagccatctccaaacca
acctactttgcccgaaaattcgatagtatggtagatatcgattcaattga
agccgccgaaatgcaatcaatttcacctgaaaaacttcaattaaatcatc
caacctatcatttcgcttttgcaaatattttcaaaactggaatcgacgag
cagaagcttcatttcgaaagtttggcgaatttcgcgctgaaatccaccga
aactcgggcaaaattccgaaaagttttgcgaatcgatgctcttcgagctc
atcataatgctctcatcgagattgtcatgaaaatcgaaacgacggacggc
gcgacgtttgaatttttgattcatagactgtcccatgtgaatttgacgga
aaatgaggagaagcttgtggagcacggatatctattgagagctgtatcgt
ttggaacaaaatttgaatggaaagaggagctttgcagggaatatatggga
tttgtcactgataacgacactcttcacacccgcttgcaatggcatccgac
agaacatgtgaaaaaagttggagacaagacgagtcccgaaatgatattca
aatatcgaaaaggcgatgagctcattgagcaaactgttgtaaagccgtac
gattcagtgtttggaggacaatttgatagttggaatgttgggaaaaaact
ctccaacctgacgacctgttccaatttcttcgtcgacatcatctccccat
cgtcacccgatgatgctccaccgctcgccacactacattttcccgtttac
actgatcaaaacgcgcattgccacgtggattacctacgccagttcttcaa
aattgccgatttttgcacttccggcgacgcttgcaaggaaaagatctgga
gtacgagctatcccgatccgaaatcagatatttttgtcggatacgatgag
gatacgcagaccttgatttag
|
Protein
MLFNGTTKYRDYAIVISLFFLLNVYLLYNTAQHTQVGNSKHISSDSGEKTSNPLPSCEIT
DDLAKSAISRAITPSCKAKLQLEACQLKNGTFTINFPENQCPNHDSRLIDQRIGCFLDKK
EARVLTEFEYKLPKSNGKATCRKHCYKAGFLYFGLEFGHECFCGNDVSNATAVDDVECRA
YKCPGNENSEEFCGGFNAVEIFRTGFRSKVNHRKPTYLPPSSDSIKNPVKILFLLQLNGR
NERQVKRFLKSIYLPHHYYYIHVDARQNYMFSEMQKVADFLDNIHITERRFSTIWGGASL
LQMFLQVIRDSMKIEKFKDWDYIINFSESDFPILPISDFERLITVNNGKSFLASHGYNTG
KFIQKQGFEYVFSECDNRMFRIGKREFPQNLRIDGGSDWVGIHRNLAEFSISDEELPRKL
RKTYESILLPLESFYHTLAFNSEFCDDLLMSNLRLTNWYRKQGCRCASLKPIVDWCGCSP
LVFREETMKKFELQKAISKPTYFARKFDSMVDIDSIEAAEMQSISPEKLQLNHPTYHFAF
ANIFKTGIDEQKLHFESLANFALKSTETRAKFRKVLRIDALRAHHNALIEIVMKIETTDG
ATFEFLIHRLSHVNLTENEEKLVEHGYLLRAVSFGTKFEWKEELCREYMGFVTDNDTLHT
RLQWHPTEHVKKVGDKTSPEMIFKYRKGDELIEQTVVKPYDSVFGGQFDSWNVGKKLSNL
TTCSNFFVDIISPSSPDDAPPLATLHFPVYTDQNAHCHVDYLRQFFKIADFCTSGDACKE
KIWSTSYPDPKSDIFVGYDEDTQTLI
|
| References |
Herman T, Horvitz HR
Cold Spring Harb. Symp. Quant. Biol.
(1997)
62
:353-9
[PMID : 9598369]
Mutations that perturb vulval invagination in C. elegans.
Herman T, Hartwieg E, Horvitz HR
Proc. Natl. Acad. Sci. U.S.A.
(1999)
96
(3)
:968-73
[PMID : 9927677]
sqv mutants of Caenorhabditis elegans are defective in vulval epithelial invagination.
Hwang HY, Olson SK, Brown JR, Esko JD, Horvitz HR
J. Biol. Chem.
(2003)
278
(14)
:11735-8
[PMID : 12584198]
The Caenorhabditis elegans genes sqv-2 and sqv-6, which are required for vulval morphogenesis, encode glycosaminoglycan galactosyltransferase II and xylosyltransferase.
Sugahara K, Mikami T, Uyama T, Mizuguchi S, Nomura K, Kitagawa H
Curr. Opin. Struct. Biol.
(2003)
13
(5)
:612-20
[PMID : 14568617]
Recent advances in the structural biology of chondroitin sulfate and dermatan sulfate.
Wang H, Spang A, Sullivan MA, Hryhorenko J, Hagen FK
Mol. Biol. Cell
(2005)
16
(9)
:4202-13
[PMID : 15987734]
The terminal phase of cytokinesis in the Caenorhabditis elegans early embryo requires protein glycosylation.
Sternberg PW
WormBook
(2005)
:1-28
[PMID : 18050418]
Vulval development.
Brunner A, Kolarich D, Voglmeir J, Paschinger K, Wilson IB
Glycoconj. J.
(2006)
23
(7-8)
:543-54
[PMID : 17006645]
Comparative characterisation of recombinant invertebrate and vertebrate peptide O-Xylosyltransferases.
Berninsone PM
WormBook
(2006)
:1-22
[PMID : 18050430]
Carbohydrates and glycosylation.
Franks DM, Izumikawa T, Kitagawa H, Sugahara K, Okkema PG
Dev. Biol.
(2006)
296
(2)
:409-20
[PMID : 16828468]
C. elegans pharyngeal morphogenesis requires both de novo synthesis of pyrimidines and synthesis of heparan sulfate proteoglycans.
Updike DL, Strome S
Genetics
(2009)
183
(4)
:1397-419
[PMID : 19805813]
A genomewide RNAi screen for genes that affect the stability, distribution and function of P granules in Caenorhabditis elegans.
Shaye DD, Greenwald I
PLoS ONE
(2011)
6
(5)
:e20085
[PMID : 21647448]
OrthoList: a compendium of C. elegans genes with human orthologs.
Berninsone PM, Hirschberg CB
Glycoconj. J.
19
(4-5)
:325-30
[PMID : 12975612]
The nematode Caenorhabditis elegans as a model to study the roles of proteoglycans.
|
| Functional Descriptions |
sqv-6
sqv-6 encodes a xylosyltransferase, active in cell culture, that is required for cytokinesis of one-cell embryos and for vulval morphogenesis; SQV-6 is predicted to begin the synthesis of glycosaminoglycans by adding xylose to their protein cores; the common requirement for SQV-6 in both cytokinesis and morphogenesis may be to promote filling an extracellular space with hygroscopic proteoglycans (either in the eggshell, or underneath the L4 cuticle), which in turn may cause the space to fill with fluid.
|
| Deletion Mutants |
n2845
tm834
|
| In Situ |
|
| Expression |
Expression
|
WBGene00005024
Phenotype
Homology_paralog
|
|
|
| Phenotype |
Definition |
RNAi / Allele |
bloated
|
"Worms appears turgid or swollen as a result of an excess number of eggs being retained in the uterus." [WB:WBPerson2021, WB:WBPerson557]
|
|
cytokinesis variant emb
|
"Any variation that disrupts the cytoplasmic division of a cell during embryonic development compared to control." [GO:0000910, WB:WBPerson2021]
|
|
egg laying defective
|
"Eggs are not laid, laid at a slower rate or eggs are laid at a later stage of development compared to control." [WB:cab, WB:WBPaper00004402, WB:WBPaper00004651, WB:WBPaper00005654, WB:WBPaper00006395, WB:WBPaper00024497, WB:WBPaper00025054]
|
|
|
embryonic lethal
|
"Animals die during embryonic development. In C. elegans, often assayed as refractile eggs that fail to hatch; when applied to large-scale RNAi screens in C. elegans, more than 10% of embryos die." [WB:cab, WB:WBPaper00000179, WB:WBPaper00004403, WB:WBPaper00004540, WB:WBPaper00004651, WB:WBPaper00004769, WB:WBPaper00005654, WB:WBPaper00024497, WB:WBPaper00024925, WB:WBPaper00025054]
|
|
hermaphrodite self sterile
|
"Hermaphrodites fail to produce any viable progeny via self-fertilization. However, such hermaphrodites can successfully reproduce if mated to control males." [WB:WBPaper00001075, WB:WBPerson2021]
|
|
hermaphrodite sterile
|
"Hermaphrodites fail to generate viable self-progeny and/or cross-progeny." [WB:WBPerson2021, WB:WBPerson557]
|
|
|
larval arrest
|
"The developmental program of the animals halts at any larval stage and thus fails to reach adulthood. In C.elegans, this occurs anytime during L1-L4 stage." [WB:WBPaper00002958, WB:WBPerson2021]
|
|
|
larval lethal
|
"The animal dies at any time between hatching and onset to adulthood." [GO:0002119, WB:WBPerson712]
|
|
life span variant
|
"Adult life span is either longer or shorter than typical of control animals." [GO:0008340, WB:cab, WB:WBPaper00005863, WB:WBPaper00026717, WB:WBPerson557]
|
|
locomotion variant
|
"Animals exhibit deviations in self-propelled movement on a solid medium compared to control animals." [GO:0040011, WB:cab, WB:WBPaper00024949, WB:WBPerson712]
|
|
|
maternal sterile
|
" Animals produce no or very few embryos as a result of experimental treatment. This is in contrast to sterility due to genetic perturbations (maternal effect sterility)." [WB:cab, WB:cgc5599, WB:cgc7141, WB:WBPerson557]
|
|
multiple nuclei early emb
|
"Embryos contain more than one nucleus per cell in the inviable one- to four-cell embryo." [WB:cab, WB:cgc5599]
|
|
neuron cell body absent misplaced
|
"The body of a neuron is not where it should be when compared to control animals; it is absent or misplaced." [WB:WBPaper00000502, WB:WBPaper00000635, WB:WBPerson712]
|
|
one cell arrest early emb
|
"Embryos fail to divide and arrest as one-cell embryos." [WB:cab, WB:cgc5599]
|
|
oocyte morphology variant
|
"Haploid female germ cells (oocytes) exhibit variations in their overall structure, appearance or contents compared to control." [WB:WBPaper00001883, WB:WBPerson2021]
|
|
|
organism morphology variant
|
"Animals exhibit variations in the form, structure or composition of any part of their anatomy compared to control animals." [WB:cab, WB:WBPaper00004402, WB:WBPaper00004403, WB:WBPaper00004651, WB:WBPaper00005654, WB:WBPaper00006395]
|
|
|
pharyngeal development variant
|
"Variations in the progression of the pharynx (feeding organ) over time, from its formation to the mature structure compared to control. In C. elegans the pharynx is divided into the anterior and posterior regions. The anterior region includes the corpus (procorpus and metacorpus - first bulb) and the posterior region includes the isthmus and terminal bulb (second bulb)." [GO:0043282, WB:WBPerson2021]
|
|
|
postembryonic development variant
|
"Any variation in the progression of an animal over time, from hatching to adulthood, compared to control." [WB:WBPerson2021]
|
|
reduced brood size
|
"The characteristic number of offspring produced is lower compared to that of control animals." [WB:WBPerson557]
|
|
|
slow growth
|
"Any variation that causes a reduction in growth rate compared to control." [WB:cab, WB:WBPaper00004402, WB:WBPaper00004403, WB:WBPaper00004651, WB:WBPaper00004769, WB:WBPaper00005654, WB:WBPaper00006395, WB:WBPaper00024497, WB:WBPerson557]
|
|
small
|
"Animals are shorter and thinner than control animals at the same developmental stage." [WB:cab, WB:cgc31]
|
|
squashed vulva
|
"The apparent partial collapse of the vulval invagination and the elongation of central vulva cells often leading to a flattened appearance." [WB:WBPaper00003405]
|
|
|
sterile progeny
|
"Any variation that compromises the reproductive ability of the progeny of an animal." [WB:WBPerson2021, WB:WBPerson557]
|
|
|
Variant
|
"Animals exhibit variations compared to a given control." [WB:WBPerson557]
|
|
vulval invagination variant L4
|
"The characteristic Christmas-tree shaped invagination formed by the terminal vulval cells at the mid-late L4 stage is altered." [WB:WBPaper00001738, WB:WBPerson2021]
|
|
