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[187997_s_at] acyl-CoA desaturase

Description VZK822L.1 /REP_DB=WormBase Gene ID /WP=CE18302 /GEN=fat-6 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=acyl-CoA desaturase
Cluster 6grp_highest_10_10 > 49      6grp_high1_10_10 > 84      4grp_highest_8_8 > 39      4grp_high_8_8 > 04      6grp_highest_nonorm > 28      6grp_total > 74      4grp_total > 04      6grp_highest_sub > 04_05_06      6grp_cgc > 67      6grp_cgc_sub > In      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 9331
1 2 3 4 range
A 11779.9
(-1.6)
P 		10184.3
(-2.8)
P 		9844.2
(-3)
P 		18433.9
(3)
P 		8590
B 13425.8
(0)
P 		9574.2
(-3)
P 		9595.9
(-3)
P 		17270
(3)
P 		7696
C 11785.7
(-1.1)
P 		9607.4
(-2.6)
P 		9102.9
(-3)
P 		17436
(3)
P 		8333
avr 12330.5
(-0.9) 		9788.6
(-2.8) 		9514.3
(-3) 		17713.3
(3) 		8199

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7228
1 2 3 4 5 6 range
A 8370.6
(-2.3)
P 		7555.8
(-3)
P 		10555.2
(-0.3)
P 		13318.7
(2.3)
P 		11571.1
(0.7)
P 		14128.3
(3)
P 		6573
B 6900.1
(-3)
P 		7835.7
(-2.1)
P 		12452.5
(2.1)
P 		13311.5
(2.9)
P 		11725.1
(1.5)
P 		13377.6
(3)
P 		6478
C 7384.9
(-2.9)
P 		7269.7
(-3)
P 		11207.1
(0.6)
P 		13464.1
(2.7)
P 		11669.1
(1)
P 		13792.2
(3)
P 		6523
avr 7551.9
(-3) 		7553.7
(-3) 		11404.9
(0.7) 		13364.8
(2.6) 		11655.1
(1) 		13766
(3) 		6214
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2078
1 2 3 4 range
A 4289
(3)
P 		2210.7
(-3)
P 		2573.5
(-2)
P 		2698.4
(-1.6)
P 		2078
B 4281.4
(3)
P 		2364.6
(-2.6)
P 		2223.6
(-3)
P 		3680.2
(1.2)
P 		2058
C 3901.4
(3)
P 		2762.2
(-3)
P 		3172.7
(-0.8)
P 		2940
(-2.1)
P 		1139
avr 4157.3
(3) 		2445.8
(-3) 		2656.6
(-2.3) 		3106.2
(-0.7) 		1712

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3445
1 2 3 4 5 6 range
A 1543.1
(-3)
P 		2687.2
(0.5)
P 		2298.7
(-0.7)
P 		3377.9
(2.6)
P 		3491.7
(3)
P 		3439.8
(2.8)
P 		1949
B 2400.9
(-3)
P 		2608.2
(-2.5)
P 		3023.8
(-1.6)
P 		3525.7
(-0.4)
P 		4763.8
(2.5)
P 		4988.4
(3)
P 		2588
C 2737.3
(-1.7)
P 		2218.2
(-3)
P 		2852.4
(-1.4)
P 		2707.6
(-1.8)
P 		3776
(0.9)
P 		4617.1
(3)
P 		2399
avr 2227.1
(-3) 		2504.5
(-2.2) 		2725
(-1.6) 		3203.7
(-0.2) 		4010.5
(2) 		4348.4
(3) 		2121
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 187997_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8934
Sequence Type Exemplar sequence
Representative Public ID VZK822L.1 NCBI
Target Description VZK822L.1 /REP_DB=WormBase Gene ID /WP=CE18302 /GEN=fat-6 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=acyl-CoA desaturase
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_069854(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069854 NCBI Caenorhabditis elegans FATty acid desaturase family member (fat-6) (fat-6) mRNA, complete cds. 11/11 None
SNAP00000028565 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11913789:11915638:-1 11/11 None
GENEFINDER00000028566 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11913789:11915727:-1 11/11 None
VZK822L.1 ENSEMBL cdna:known chromosome:CEL140:IV:11913189:11915657:-1 gene:VZK822L.1 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:11913794-11915644(-) 100.0 100.0
Public Domain and Genome References
Gene Title acyl-CoA desaturase
Gene Symbol fat-6
Ensembl VZK822L.1
Entrez Gene 178122 Entrez gene
SwissProt O01708 EMBL-EBI
WormBase CE18302 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:258267_AT fatty acid desaturase family protein at
DROSOPHILA_2:1637550_AT dm
DROSGENOME1:149777_AT dm
MOUSE430A_2:1423366_AT stearoyl-coenzyme A desaturase 3 mm
MOE430A:1423366_AT stearoyl-coenzyme A desaturase 3 mm
MOUSE430_2:1423366_AT stearoyl-coenzyme A desaturase 3 mm
MG-U74CV2:138407_F_AT stearoyl-coenzyme A desaturase 3 mm
MOE430A:1450956_AT stearoyl-coenzyme A desaturase 3 mm
MOUSE430A_2:1450956_AT stearoyl-coenzyme A desaturase 3 mm
MOUSE430_2:1450956_AT stearoyl-coenzyme A desaturase 3 mm
MU19KSUBC:TC38959_AT Fatty acid desaturase (Scd3) mm
MU19KSUBC:TC38959_G_AT Fatty acid desaturase (Scd3) mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6633 fatty acid biosynthesis inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5783 endoplasmic reticulum inferred from electronic annotation QuickGO AmiGO
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4768 stearoyl-CoA 9-desaturase activity inferred from electronic annotation QuickGO AmiGO
5506 iron ion binding inferred from electronic annotation QuickGO AmiGO
16491 oxidoreductase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB08356 Hypothetical protein VZK822L.1 [Caenorhabditis elegans] ref|NP_502255.1| FATty acid desaturase family member (fat-6) [Caenorhabditis elegans] gb|AAF97550.1| stearoyl-CoA desaturase FAT-6 [Caenorhabditis elegans] 0.0
blast CAE62144 Hypothetical protein CBG06190 [Caenorhabditis briggsae] 1.0E-175
blast CAE62144 Hypothetical protein CBG06190 [Caenorhabditis briggsae] 1.0E-174
blast NP_504814 FATty acid desaturase family member (fat-7) [Caenorhabditis elegans] gb|AAC48239.1| Fatty acid desaturase protein 7 [Caenorhabditis elegans] gb|AAF97549.1| stearoyl-CoA desaturase FAT-7 [Caenorhabditis elegans] 1.0E-172
Protein Domains
Database ID Description E-Value
Pfam IPR005804 EMBL-EBI Fatty acid desaturase 2.3E-79
Pfam IPR005804 EMBL-EBI Fatty acid desaturase 2.3E-79
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502255.1 4 47-69,79-101,196-215,219-241
VZK822L.1 4 47-69,79-101,196-215,219-241
SNAP00000028565 4 47-69,79-101,196-215,219-241
GENEFINDER00000028566 4 77-99,109-131,226-245,249-271
Sequence
Target Sequence 
>C. ELEGANS:187997_S_AT
ggagccaagcttgacatgtctgatctcttgagtgacccagttctcgtcttccagagaaaa
cattacttcccacttgtcatcttgtgctgcttcattcttccaacaattatcccagtttac
ttctggaaggagactgcattcattgccttctacacagctggaacattccgttattgcttc
acacttcatgctacatggtgcatcaacagcgctgctcactatttcggatggaagccatac
gattcctcaattaccccagtcgaaaacgtcttcaccacaattgctgccgtcggagaggga
ggtcacaacttccatcacacattcccacaagactacagaacatctgaatactcattgaaa
tacaattggacacgtgtccttattgatactgcagctgctcttggacttgtctacgaccgg
aaaactgcttgtgatgagattatcggccggcaggtatccaatca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGCCAAGCTTGACATGTCTGATC 665 521 532 Antisense
GTCTGATCTCTTGAGTGACCCAGTT 277 471 549 Antisense
TTCATTGCCTTCTACACAGCTGGAA 506 689 670 Antisense
TTGCTTCACACTTCATGCTACATGG 679 701 705 Antisense
GAAGCCATACGATTCCTCAATTACC 17 345 762 Antisense
TCCTCAATTACCCCAGTCGAAAACG 692 589 775 Antisense
CGAAAACGTCTTCACCACAATTGCT 404 249 792 Antisense
AGAGGGAGGTCACAACTTCCATCAC 594 67 825 Antisense
GGACACGTGTCCTTATTGATACTGC 40 527 899 Antisense
CTCTTGGACTTGTCTACGACCGGAA 442 229 929 Antisense
TTATCGGCCGGCAGGTATCCAATCA 487 679 971 Antisense
Sequence Source Affymetrix Proprietary Database