P34766 (PAL1_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Homeobox protein pal-1

Alternative name(s):
Caudal homolog 1
Homeobox protein ceh-3
Posterior alae in males protein 1

Gene names

Name:	pal-1
Synonyms:	ceh-3
ORF Names:	C38D4.6

Organism

Caenorhabditis elegans

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length	270 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Transcriptional activator. Interacts with promoter regions for tbx-8.9, tbx-9, elt-1, hnd-1, scrt-1, and vab-7 genes. Binds the sequence ATTTATGAC. Binds to the enhancer region of the hlh-1 gene promoter during embryonic body wall muscle development. Activates the gene for mab-5 in embryo development. Necessary for vab-7 expression in C blastomeres in the posterior of embryos. Required for posterior V6 neuroectoblast cell fate specification during postembryonic neurogenesis (patterning) which generates the characteristic ray lineage during male tail development. Binds to ced-3 promoter and activated expression which is crucial for tail-spike cell death. Has a role in E cell specification in endoderm development and body wall muscle development. Ref.1 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.14 Ref.15 Ref.16 Ref.18 Ref.19 Ref.20
Subunit structure	Interacts with tir-1 and let-756. Ref.13 Ref.17
Subcellular location	Nucleus. Chromosome › centromere › kinetochore. Chromosome. Note: Localized to condensed chromosomes. Ref.5
Tissue specificity	Blastomeres. Embryo. Oocytes. Ref.5 Ref.7 Ref.10 Ref.11
Developmental stage	Expressed both maternally and zygotically. Expression observed at the 4 cell embryo in posterior blastomeres. Detected in all descendants of EMS and P2 blastomeres. During gastrulation and morphogenesis expression is seen sporadically in all major cell lineages except the germ line. Ref.5 Ref.10
Induction	By heat shock. Ref.8
Disruption phenotype	Embryos shows disorganization of cell types and lack specfication. Loss of V6 rays development in mail tail. C and D blastomere dervied muscle. Ref.1 Ref.4 Ref.12 Ref.18
Miscellaneous	Fifth intron is thought to contain a regulatory element required for expression in postembryonic neuroblast V6 cells. 3'-UTR thought to inhibit self-translation in anterior blastomeres.
Sequence similarities	Belongs to the Caudal homeobox family. Contains 1 homeobox DNA-binding domain.
Sequence caution	The sequence CAA44619.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Centromere Chromosome Kinetochore Nucleus
Coding sequence diversity	Alternative splicing
Domain	Homeobox
Ligand	DNA-binding
Molecular function	Activator Developmental protein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ectodermal cell fate commitment Inferred from mutant phenotype Ref.5. Source: WormBase embryo development ending in birth or egg hatching Inferred from mutant phenotype. Source: WormBase embryonic pattern specification Inferred from mutant phenotype Ref.5. Source: WormBase muscle cell fate commitment Inferred from mutant phenotype Ref.5. Source: WormBase positive regulation of transcription from RNA polymerase II promoter Inferred from direct assay. Source: WormBase
Cellular component	condensed chromosome kinetochore Inferred from electronic annotation. Source: UniProtKB-SubCell condensed nuclear chromosome Inferred from direct assay Ref.5. Source: WormBase
Molecular function	protein binding Inferred from physical interaction. Source: IntAct sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro sequence-specific distal enhancer binding RNA polymerase II transcription factor activity Inferred from direct assay. Source: WormBase
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
emb-30	P34441	2	EBI-311911,EBI-311903

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform a (identifier: P34766-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform b (identifier: P34766-2)

The sequence of this isoform differs from the canonical sequence as follows:
     166-167: Missing.

Note: No experimental confirmation available.

Isoform c (identifier: P34766-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-46: Missing.
     166-167: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 270	270	Homeobox protein pal-1		PRO_0000049234
Regions
	DNA binding	206 – 265	60	Homeobox
	Compositional bias	137 – 143	7	Poly-Ala
Natural variations
	Alternative sequence	1 – 46	46	Missing in isoform c.		VSP_039082
	Alternative sequence	166 – 167	2	Missing in isoform b and isoform c.		VSP_039083

Sequences

	Sequence		Length	Mass (Da)
	Isoform a [UniParc]. Last modified May 18, 2010. Version 2. Checksum: 8ECBD30E71892A77	FASTA	270	30,334
	10 20 30 40 50 60 MSVDVKSDFS ENESSSTPSP TTVPADVTWP HYPMMPFMQP HPLREKMLQP TFDPQIYGRW 70 80 90 100 110 120 SQMGDTGFYG HPDLYPFGLP QLAANGQIPA VEAVDVKPPL SNGSSSSDSG MYPSPSDMMT 130 140 150 160 170 180 PFPSTSSGAA SSSELSAAAA AAANYQMRAA TCYQQSVWPF MDYQQFQGFS WKMPLGNNHG 190 200 210 220 230 240 KDRRSSSDGK TLPTGPGTNN VRVRTADKYR MVYSDYQRLE LEKEFHTSPF ITSDRKSQLS 250 260 270 TMLSLTERQI KIWFQNRRAK DRRDKQKIRL
	Isoform b [UniParc]. Checksum: 770F1FAA1A21CCCA	FASTA	268	30,059
	10 20 30 40 50 60 MSVDVKSDFS ENESSSTPSP TTVPADVTWP HYPMMPFMQP HPLREKMLQP TFDPQIYGRW 70 80 90 100 110 120 SQMGDTGFYG HPDLYPFGLP QLAANGQIPA VEAVDVKPPL SNGSSSSDSG MYPSPSDMMT 130 140 150 160 170 180 PFPSTSSGAA SSSELSAAAA AAANYQMRAA TCYQQSVWPF MDYQQGFSWK MPLGNNHGKD 190 200 210 220 230 240 RRSSSDGKTL PTGPGTNNVR VRTADKYRMV YSDYQRLELE KEFHTSPFIT SDRKSQLSTM 250 260 LSLTERQIKI WFQNRRAKDR RDKQKIRL
	Isoform c [UniParc]. Checksum: C794EC0B8C2888CD	FASTA	222	24,857
	10 20 30 40 50 60 MLQPTFDPQI YGRWSQMGDT GFYGHPDLYP FGLPQLAANG QIPAVEAVDV KPPLSNGSSS 70 80 90 100 110 120 SDSGMYPSPS DMMTPFPSTS SGAASSSELS AAAAAAANYQ MRAATCYQQS VWPFMDYQQG 130 140 150 160 170 180 FSWKMPLGNN HGKDRRSSSD GKTLPTGPGT NNVRVRTADK YRMVYSDYQR LELEKEFHTS 190 200 210 220 PFITSDRKSQ LSTMLSLTER QIKIWFQNRR AKDRRDKQKI RL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Regulation of cellular responsiveness to inductive signals in the developing C. elegans nervous system." Waring D.A., Kenyon C. Nature 350:712-715(1991) [PubMed: 2023634] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A), FUNCTION, DISRUPTION PHENOTYPE. Strain: Bristol N2.
[2]	"Genome sequence of the nematode C. elegans: a platform for investigating biology." The C. elegans sequencing consortium Science 282:2012-2018(1998) [PubMed: 9851916] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING. Strain: Bristol N2.
[3]	"Caenorhabditis elegans has scores of homoeobox-containing genes." Buerglin T.R., Finney M., Coulson A., Ruvkun G. Nature 341:239-243(1989) [PubMed: 2571091] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 198-268 (ISOFORMS A/B/C). Strain: Bristol N2.
[4]	"Selective silencing of cell communication influences anteroposterior pattern formation in C. elegans." Waring D.A., Kenyon C. Cell 60:123-131(1990) [PubMed: 2295086] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[5]	"Spatial and temporal controls target pal-1 blastomere-specification activity to a single blastomere lineage in C. elegans embryos." Hunter C.P., Kenyon C. Cell 87:217-226(1996) [PubMed: 8861906] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
[6]	"A C. elegans Hox gene switches on, off, on and off again to regulate proliferation, differentiation and morphogenesis." Salser S.J., Kenyon C. Development 122:1651-1661(1996) [PubMed: 8625851] [Abstract] Cited for: FUNCTION.
[7]	"The maternal par genes and the segregation of cell fate specification activities in early Caenorhabditis elegans embryos." Bowerman B., Ingram M.K., Hunter C.P. Development 124:3815-3826(1997) [PubMed: 9367437] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY.
[8]	"Maternal control of a zygotic patterning gene in Caenorhabditis elegans." Ahringer J. Development 124:3865-3869(1997) [PubMed: 9367442] [Abstract] Cited for: FUNCTION, INDUCTION BY HEAT SHOCK, TISSUE SPECIFICATION.
[9]	"A C. elegans mediator protein confers regulatory selectivity on lineage-specific expression of a transcription factor gene." Zhang H., Emmons S.W. Genes Dev. 14:2161-2172(2000) [PubMed: 10970880] [Abstract] Cited for: FUNCTION, MISCELLANEOUS.
[10]	"Zygotic expression of the caudal homolog pal-1 is required for posterior patterning in Caenorhabditis elegans embryogenesis." Edgar L.G., Carr S., Wang H., Wood W.B. Dev. Biol. 229:71-88(2001) [PubMed: 11133155] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
[11]	"MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans." Huang N.N., Mootz D.E., Walhout A.J., Vidal M., Hunter C.P. Development 129:747-759(2002) [PubMed: 11830574] [Abstract] Cited for: TISSUE SPECIFICITY.
[12]	"Polycomb group regulation of Hox gene expression in C. elegans." Ross J.M., Zarkower D. Dev. Cell 4:891-901(2003) [PubMed: 12791273] [Abstract] Cited for: DISRUPTION PHENOTYPE.
[13]	"TLR-independent control of innate immunity in Caenorhabditis elegans by the TIR domain adaptor protein TIR-1, an ortholog of human SARM." Couillault C., Pujol N., Reboul J., Sabatier L., Guichou J.-F., Kohara Y., Ewbank J.J. Nat. Immunol. 5:488-494(2004) [PubMed: 15048112] [Abstract] Cited for: INTERACTION WITH TIR-1.
[14]	"The Wnt effector POP-1 and the PAL-1/Caudal homeoprotein collaborate with SKN-1 to activate C. elegans endoderm development." Maduro M.F., Kasmir J.J., Zhu J., Rothman J.H. Dev. Biol. 285:510-523(2005) [PubMed: 16084508] [Abstract] Cited for: FUNCTION.
[15]	"The myogenic potency of HLH-1 reveals wide-spread developmental plasticity in early C. elegans embryos." Fukushige T., Krause M. Development 132:1795-1805(2005) [PubMed: 15772130] [Abstract] Cited for: FUNCTION.
[16]	"The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo." Baugh L.R., Hill A.A., Claggett J.M., Hill-Harfe K., Wen J.C., Slonim D.K., Brown E.L., Hunter C.P. Development 132:1843-1854(2005) [PubMed: 15772128] [Abstract] Cited for: FUNCTION.
[17]	"Direct and heterologous approaches to identify the LET-756/FGF interactome." Popovici C., Berda Y., Conchonaud F., Harbis A., Birnbaum D., Roubin R. BMC Genomics 7:105-105(2006) [PubMed: 16672054] [Abstract] Cited for: INTERACTION WITH LET-756.
[18]	"Specification of the C. elegans MS blastomere by the T-box factor TBX-35." Broitman-Maduro G., Lin K.T., Hung W.W., Maduro M.F. Development 133:3097-3106(2006) [PubMed: 16831832] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[19]	"Timing of the onset of a developmental cell death is controlled by transcriptional induction of the C. elegans ced-3 caspase-encoding gene." Maurer C.W., Chiorazzi M., Shaham S. Development 134:1357-1368(2007) [PubMed: 17329362] [Abstract] Cited for: FUNCTION.
[20]	"Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression." Yanai I., Baugh L.R., Smith J.J., Roehrig C., Shen-Orr S.S., Claggett J.M., Hill A.A., Slonim D.K., Hunter C.P. Mol. Syst. Biol. 4:163-163(2008) [PubMed: 18277379] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X62782 mRNA. Translation: CAA44619.1. Different initiation. Z46241 Genomic DNA. Translation: CAA86322.2. Z46241 Genomic DNA. Translation: CAH19082.1. Z46241 Genomic DNA. Translation: CBG22736.1. X57140 mRNA. Translation: CAA40419.1.
PIR	S15091. T19829.
RefSeq	NP_001021209.1. NM_001026038.3. NP_001021210.1. NM_001026039.2.
UniGene	Cel.18383.
3D structure databases
ProteinModelPortal	P34766.
SMR	P34766. Positions 206-267.
ModBase	Search...
Protein-protein interaction databases
IntAct	P34766. 51 interactions.
MINT	MINT-213983.
STRING	P34766.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	C38D4.6a.1; C38D4.6a.1; C38D4.6. C38D4.6a.2; C38D4.6a.2; C38D4.6.
GeneID	175638.
KEGG	cel:C38D4.6.
UCSC	C38D4.6a.2. c. elegans.
Organism-specific databases
CTD	175638.
WormBase	C38D4.6a; CE27837; WBGene00003912; pal-1.
Phylogenomic databases
eggNOG	meNOG14780.
GeneTree	EMGT00050000001991.
HOGENOM	HBG381642.
InParanoid	P34766.
OMA	DRRDKQK.
PhylomeDB	P34766.
Gene expression databases
ArrayExpress	P34766.
Family and domain databases
InterPro	IPR001356. Homeobox. IPR017970. Homeobox_CS. IPR009057. Homeodomain-like. IPR012287. Homeodomain-rel. [Graphical view]
Gene3D	G3DSA:1.10.10.60. Homeodomain-rel. 1 hit.
KO	K09312.
Pfam	PF00046. Homeobox. 1 hit. [Graphical view]
SMART	SM00389. HOX. 1 hit. [Graphical view]
SUPFAM	SSF46689. Homeodomain_like. 1 hit.
PROSITE	PS00027. HOMEOBOX_1. 1 hit. PS50071. HOMEOBOX_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PAL1_CAEEL

Accession

Primary (citable) accession number: P34766
Secondary accession number(s): C9IY23, Q18513, Q65ZB9

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	May 18, 2010
Last modified:	December 14, 2011
This is version 102 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project