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[192190_at] 3-hydroxyacyl-CoA dehydrogenase

Description R09B5.6 /REP_DB=WormBase Gene ID /WP=CE12628 /TR=O44608 /GB=AAB94215.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=3-hydroxyacyl-CoA dehydrogenase
Cluster 6grp_highest_10_10 > 38      6grp_high1_10_10 > 72      4grp_highest_8_8 > 12      4grp_high_8_8 > 31      6grp_highest_nonorm > 28      6grp_total > 73      4grp_total > 24      6grp_highest_sub > 04      6grp_cgc > 75      6grp_high1_sub > 04      6grp_cgc_sub > 03_04      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3109
1 2 3 4 range
A 357.9
(-3)
P 		1693.6
(-0.2)
P 		3170
(3)
P 		3122.4
(2.9)
P 		2812
B 411.2
(-3)
P 		1669.3
(-0.4)
P 		2670.8
(1.7)
P 		3305.8
(3)
P 		2895
C 352.9
(-3)
P 		1809.6
(-0.2)
P 		2929.2
(2)
P 		3462.3
(3)
P 		3109
avr 374
(-3) 		1724.2
(-0.2) 		2923.3
(2.2) 		3296.8
(3) 		2923

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 12417
1 2 3 4 5 6 range
A 3845.5
(-3)
P 		8911.9
(0.9)
P 		11582.3
(3)
P 		11530.3
(3)
P 		10793.1
(2.4)
P 		8887
(0.9)
P 		7737
B 3589
(-3)
P 		8357.7
(0.2)
P 		12547.1
(3)
P 		10138.6
(1.4)
P 		10906.7
(1.9)
P 		7689.8
(-0.3)
P 		8958
C 3604.3
(-3)
P 		8239
(-0.8)
P 		14142.2
(2.1)
P 		16005.9
(3)
P 		11003.9
(0.6)
P 		8492.8
(-0.6)
P 		12402
avr 3679.6
(-3) 		8502.9
(0.2) 		12757.2
(3) 		12558.3
(2.9) 		10901.2
(1.8) 		8356.5
(0.1) 		9078
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 904
1 2 3 4 range
A 130.3
(-3)
P 		367.6
(-1)
P 		828.7
(3)
P 		457.1
(-0.2)
P 		698
B 131.1
(-3)
P 		412.3
(-0.1)
P 		618.9
(2.1)
P 		704.5
(3)
P 		573
C 116.8
(-3)
P 		520.3
(-0.3)
P 		1020.9
(3)
P 		583.8
(0.1)
P 		904
avr 126.1
(-3) 		433.4
(-0.4) 		822.8
(3) 		581.8
(0.9) 		697

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3722
1 2 3 4 5 6 range
A 708.9
(-3)
P 		3169.5
(2.8)
P 		2522.4
(1.3)
P 		2924.3
(2.2)
P 		3256.9
(3)
P 		2163.7
(0.4)
P 		2548
B 1248.8
(-3)
P 		2781.9
(-0.1)
P 		3046.8
(0.4)
P 		2685.4
(-0.3)
P 		4431.3
(3)
P 		2867.5
(0.1)
P 		3183
C 1336
(-3)
P 		2514
(0.1)
P 		3599.4
(3)
P 		3218.8
(2)
P 		3560.7
(2.9)
P 		2843
(1)
P 		2263
avr 1097.9
(-3) 		2821.8
(0.9) 		3056.2
(1.4) 		2942.8
(1.2) 		3749.6
(3) 		2624.7
(0.5) 		2652
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192190_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15622
Sequence Type Exemplar sequence
Representative Public ID R09B5.6 NCBI
Target Description R09B5.6 /REP_DB=WormBase Gene ID /WP=CE12628 /TR=O44608 /GB=AAB94215.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=3-hydroxyacyl-CoA dehydrogenase
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_071020(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_071020 NCBI Caenorhabditis elegans R09B5.6 (R09B5.6) mRNA, complete cds. 11/11 None
SNAP00000025911 ENSEMBL cdna:SNAP chromosome:CEL140:V:1460274:1461339:1 11/11 None
GENEFINDER00000025922 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:1460217:1461339:1 11/11 None
R09B5.6.2 ENSEMBL cdna:known chromosome:CEL140:V:1460196:1461438:1 gene:R09B5.6 11/11 None
R09B5.6.1 ENSEMBL cdna:known chromosome:CEL140:V:1460198:1461444:1 gene:R09B5.6 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
chrV:1460216-1461339(+) 100.0 100.0
Public Domain and Genome References
Gene Title 3-hydroxyacyl-CoA dehydrogenase
Gene Symbol hacd-1
Ensembl R09B5.6
Entrez Gene 178638 Entrez gene
SwissProt O44608 EMBL-EBI
WormBase CE12628 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6631 fatty acid metabolism inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
16491 oxidoreductase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_503421 R09B5.6 [Caenorhabditis elegans] gb|AAB94215.1| Hypothetical protein R09B5.6 [Caenorhabditis elegans] 1.0E-159
blast NP_503421 R09B5.6 [Caenorhabditis elegans] gb|AAB94215.1| Hypothetical protein R09B5.6 [Caenorhabditis elegans] 1.0E-148
blast CAE62470 Hypothetical protein CBG06566 [Caenorhabditis briggsae] 1.0E-145
blast CAE62470 Hypothetical protein CBG06566 [Caenorhabditis briggsae] 1.0E-137
Protein Domains
Database ID Description E-Value
Pfam IPR006108 EMBL-EBI 3-hydroxyacyl-CoA dehydrogenase, C-terminal 5.3E-49
Pfam IPR006176 EMBL-EBI 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 1.0E-54
Pfam IPR006108 EMBL-EBI 3-hydroxyacyl-CoA dehydrogenase, C-terminal 5.3E-49
Pfam IPR006176 EMBL-EBI 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 2.9E-50
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503421.1 1 12-34
R09B5.6.2 1 12-34
R09B5.6.1 1 12-34
GENEFINDER00000025922 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:192190_AT
tccgctgccgaagatgctgcaatggcgattgaggctgtggccgaaaacttggatctgaaa
cttgacatcttccagacaattcagaaaacttgcccacaaaactgcatgcttatcacgaac
acctcgtctctaaaactgtctcaaatgctcccagttattcagaacccggcactattcgct
gggcttcatttcttcaaccctgttccagtgatgaagcttgtagaagttgtatcaactgat
gaaacttctccagagaccacaaatttcttgttcaacttctgcaaagaaatcaaaaagctg
ccggtcgccgcgaaggatactcctggattcattgtcaaccggctattgatcccatatctt
atggactccattcgcatgctggaacgtggagatgcaactaaagaagatatcgatacagcc
atgcgatttggaacttcttacccaatgggaccaattgaattgtgtgactatgttggactt
gatgttctgcagagcactttgaaaatcttccgcgaaaccatccctggtgacgcccgtttt
gcaccaatcccacttatggaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCGCTGCCGAAGATGCTGCAATGG 10 597 292 Antisense
GGATCTGAAACTTGACATCTTCCAG 502 511 342 Antisense
AACTTGCCCACAAAACTGCATGCTT 140 139 378 Antisense
GAACACCTCGTCTCTAAAACTGTCT 619 337 408 Antisense
AGTTATTCAGAACCCGGCACTATTC 445 63 444 Antisense
TTTCTTCAACCCTGTTCCAGTGATG 249 671 480 Antisense
GAAATCAAAAAGCTGCCGGTCGCCG 195 359 577 Antisense
AACCGGCTATTGATCCCATATCTTA 258 147 628 Antisense
GGACTCCATTCGCATGCTGGAACGT 618 523 654 Antisense
GTTGGACTTGATGTTCTGCAGAGCA 119 437 763 Antisense
TTTGCACCAATCCCACTTATGGACA 228 669 829 Antisense
Sequence Source Affymetrix Proprietary Database