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[194117_at] Carbamoyl-phosphate synthase (CPSase) (2 domains), Biotin-requiring enzymes, Carboxyl transferase domain

Description T28F3.5 /REP_DB=WormBase Gene ID /WP=CE20115 /TR=Q9XUC3 /GB=CAB05298.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Carbamoyl-phosphate synthase (CPSase) (2 domains), Biotin-requiring enzymes, Carboxyl transferase domain
Cluster 6grp_total > 06      4grp_total > 47      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13
1 2 3 4 range
A 3
(-2.9)
A 		3.7
(-2.5)
A 		12.4
(3)
A 		2.9
(-3)
A 		10
B 6.4
(1.5)
A 		7.9
(3)
A 		1.7
(-3)
A 		7.3
(2.4)
A 		6
C 14.4
(3)
A 		5
(-1.5)
A 		1.8
(-3)
A 		7
(-0.5)
A 		13
avr 7.9
(3) 		5.5
(-2.5) 		5.3
(-3) 		5.7
(-2.1) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 29
1 2 3 4 5 6 range
A 32
(3)
A 		21.9
(0.7)
A 		5.3
(-3)
A 		12.1
(-1.5)
A 		10.9
(-1.7)
A 		5.7
(-2.9)
A 		27
B 3.1
(-3)
A 		6.2
(-1.3)
A 		14
(3)
A 		9.5
(0.5)
A 		6.9
(-0.9)
A 		5.5
(-1.7)
A 		11
C 9.6
(3)
A 		5.4
(-1.2)
A 		4.2
(-2.4)
A 		3.6
(-3)
A 		5.5
(-1.1)
A 		7.6
(1)
A 		6
avr 14.9
(3) 		11.2
(0.4) 		7.8
(-2) 		8.4
(-1.5) 		7.8
(-2) 		6.3
(-3) 		9
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4
1 2 3 4 range
A 1.1
(-1.6)
A 		0.8
(-2.2)
A 		3.3
(3)
A 		0.4
(-3)
A 		3
B 2
(3)
A 		2
(3)
A 		0.4
(-3)
A 		1.6
(1.5)
A 		2
C 4.8
(3)
A 		1.4
(-1.9)
A 		0.6
(-3)
A 		1.2
(-2.1)
A 		4
avr 2.6
(3) 		1.4
(-1.8) 		1.4
(-1.8) 		1.1
(-3) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7
1 2 3 4 5 6 range
A 5.9
(1.3)
A 		7.8
(3)
A 		1.2
(-3)
A 		3.1
(-1.3)
A 		3.3
(-1.1)
A 		1.4
(-2.8)
A 		7
B 1.1
(-3)
A 		2.1
(-0.4)
A 		3.4
(3)
A 		2.5
(0.7)
A 		2.8
(1.4)
A 		2.1
(-0.4)
A 		2
C 3.6
(3)
A 		1.6
(-1.1)
A 		1.1
(-2.2)
A 		0.7
(-3)
A 		1.8
(-0.7)
A 		2.5
(0.7)
A 		3
avr 3.5
(2.1) 		3.8
(3) 		1.9
(-3) 		2.1
(-2.4) 		2.6
(-0.8) 		2
(-2.7) 		2
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194117_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8543
Sequence Type Exemplar sequence
Representative Public ID T28F3.5 NCBI
Target Description T28F3.5 /REP_DB=WormBase Gene ID /WP=CE20115 /TR=Q9XUC3 /GB=CAB05298.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Carbamoyl-phosphate synthase (CPSase) (2 domains), Biotin-requiring enzymes, Carboxyl transferase domain
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_070671(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070671 NCBI Caenorhabditis elegans T28F3.5 (T28F3.5) mRNA, complete cds. 11/11 None
SNAP00000032160 ENSEMBL cdna:SNAP chromosome:CEL140:IV:17294748:17300443:1 9/11 None
GENEFINDER00000032165 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17294748:17300675:1 11/11 None
T28F3.5 ENSEMBL cdna:known chromosome:CEL140:IV:17294748:17300675:1 gene:T28F3.5 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:17294753-17300681(+) 98.83 100.0
Public Domain and Genome References
Gene Title Carbamoyl-phosphate synthase (CPSase) (2 domains), Biotin-requiring enzymes, Carboxyl transferase domain
Ensembl T28F3.5
Entrez Gene 178510 Entrez gene
SwissProt Q9XUC3 EMBL-EBI
WormBase CE20115 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
8152 metabolism inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
9343 biotin carboxylase complex inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4075 biotin carboxylase activity inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
16874 ligase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB05298 Hypothetical protein T28F3.5 [Caenorhabditis elegans] ref|NP_503072.1| T28F3.5 [Caenorhabditis elegans] 0.0
blast CAE57419 Hypothetical protein CBG00376 [Caenorhabditis briggsae] 0.0
blast CAE63310 Hypothetical protein CBG07699 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005482 EMBL-EBI Biotin carboxylase, C-terminal 8.3E-46
Pfam IPR005481 EMBL-EBI Carbamoyl-phosphate synthetase large chain, N-terminal 5.8E-22
Pfam IPR005479 EMBL-EBI Carbamoyl-phosphate synthase L chain, ATP-binding 8.1E-74
Pfam IPR000022 EMBL-EBI Carboxyl transferase 2.3E-82
Pfam IPR000022 EMBL-EBI Carboxyl transferase 4.2E-93
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503072.1 1 1623-1645
T28F3.5 1 1623-1645
GENEFINDER00000032165 1 1623-1645
Sequence
Target Sequence 
>C. ELEGANS:194117_AT
tatggtacccggaatcagcgttcaaaacatcccaagcaatatctgacttcaatcgggaat
ctcttccacttataatgattgcaagtcttcgtggattctctggaggacgaaaagacatgt
cagatcaagttcttacttttggagctcacattatcgatgaactgtcacaatatcaacaac
ctagtgccttcaaaaaagggtgtgtcgaattcgccgacatgcacgatcgttggcagcgaa
tggatcatgttggagcaattcgtcaagttgtgacgcttcaaaaaactcgagatgtcttct
ggaaaattctacgtcgagaaatgattctgatagagatggcaagaagattccaaaaggctc
caatctatccaaaaccttcactatcggaggctcttgattgggttcaaaagaagattgatg
gcgtcgataacttagagcaattctacaatcaatttttttctgaagcggtttctgcggaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATGGTACCCGGAATCAGCGTTCAA 12 655 4358 Antisense
AGCGTTCAAAACATCCCAAGCAATA 244 55 4374 Antisense
TTCAATCGGGAATCTCTTCCACTTA 618 681 4405 Antisense
TGCAAGTCTTCGTGGATTCTCTGGA 378 575 4437 Antisense
AAGTTCTTACTTTTGGAGCTCACAT 207 157 4484 Antisense
ACAATATCAACAACCTAGTGCCTTC 151 113 4524 Antisense
GGGTGTGTCGAATTCGCCGACATGC 642 495 4555 Antisense
CCGACATGCACGATCGTTGGCAGCG 258 263 4571 Antisense
AGGCTCCAATCTATCCAAAACCTTC 471 51 4712 Antisense
AAACCTTCACTATCGGAGGCTCTTG 316 125 4729 Antisense
TTTTTCTGAAGCGGTTTCTGCGGAA 31 675 4812 Antisense
Sequence Source Affymetrix Proprietary Database