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[190310_s_at] Zinc finger, C2H2 type

Description T21C9.2 /REP_DB=WormBase Gene ID /WP=CE06472 /TR=Q22639 /GB=CAA97331.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C2H2 type
Cluster 6grp_highest_10_10 > 06      6grp_high1_10_10 > 60      4grp_highest_8_8 > 50      4grp_high_8_8 > 41      6grp_highest_nonorm > 74      6grp_total > 60      4grp_total > 54      6grp_highest_sub > 04      6grp_cgc > 94      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 425
1 2 3 4 range
A 706.7
(3)
P 		410.7
(-1.5)
P 		355.5
(-2.3)
P 		311.7
(-3)
P 		395
B 656.2
(3)
P 		385.8
(-1.5)
P 		348.1
(-2.1)
P 		293.4
(-3)
P 		363
C 706.6
(3)
P 		420.1
(-1)
P 		473.5
(-0.3)
P 		281.8
(-3)
P 		425
avr 689.8
(3) 		405.5
(-1.3) 		392.4
(-1.5) 		295.6
(-3) 		394

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 401
1 2 3 4 5 6 range
A 703.1
(-1.3)
P 		648.4
(-3)
P 		656.2
(-2.8)
P 		838.7
(3)
P 		696.6
(-1.5)
P 		658.7
(-2.7)
P 		190
B 793.7
(1.6)
P 		768.2
(0.7)
P 		833.2
(3)
P 		808.2
(2.1)
P 		660.5
(-3)
P 		685.2
(-2.1)
P 		173
C 694.9
(-1)
P 		749.1
(-0.2)
P 		730.2
(-0.5)
P 		962.7
(3)
P 		561.7
(-3)
P 		644.9
(-1.8)
P 		401
avr 730.6
(-0.6) 		721.9
(-0.9) 		739.9
(-0.4) 		869.9
(3) 		639.6
(-3) 		662.9
(-2.4) 		230
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 212
1 2 3 4 range
A 257.3
(3)
P 		89.2
(-1.8)
P 		92.9
(-1.7)
P 		45.6
(-3)
P 		212
B 209.3
(3)
P 		95.3
(-1.7)
P 		80.7
(-2.3)
P 		62.5
(-3)
P 		147
C 233.9
(3)
P 		120.8
(-0.6)
P 		165
(0.8)
P 		47.5
(-3)
P 		186
avr 233.5
(3) 		101.8
(-1.4) 		112.9
(-1) 		51.9
(-3) 		182

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 147
1 2 3 4 5 6 range
A 129.6
(-3)
P 		230.6
(3)
P 		142.9
(-2.2)
P 		212.7
(1.9)
P 		210.2
(1.8)
P 		160.4
(-1.2)
P 		101
B 276.2
(3)
P 		255.7
(1.3)
P 		202.3
(-3)
P 		214.1
(-2)
P 		268.3
(2.4)
P 		255.5
(1.3)
P 		74
C 257.6
(3)
P 		228.6
(0.7)
P 		185.8
(-2.7)
P 		193.6
(-2.1)
P 		181.8
(-3)
P 		215.9
(-0.3)
P 		76
avr 221.1
(1.3) 		238.3
(3) 		177
(-3) 		206.8
(-0.1) 		220.1
(1.2) 		210.6
(0.3) 		61
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190310_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12195
Sequence Type Exemplar sequence
Representative Public ID T21C9.2 NCBI
Target Description T21C9.2 /REP_DB=WormBase Gene ID /WP=CE06472 /TR=Q22639 /GB=CAA97331.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C2H2 type
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_073310(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073310 NCBI Caenorhabditis elegans related to yeast Vacuolar Protein Sorting factor family member (vps-54) (vps-54) mRNA, complete cds. 11/11 None
SNAP00000011979 ENSEMBL cdna:SNAP chromosome:CEL140:V:10569237:10571626:-1 11/11 None
GENEFINDER00000012003 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10569237:10573936:-1 11/11 None
T21C9.2 ENSEMBL cdna:known chromosome:CEL140:V:10568985:10579001:-1 gene:T21C9.2 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:10569236-10578988(-) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C2H2 type
Gene Symbol vps-54
Ensembl T21C9.2
Entrez Gene 179473 Entrez gene
SwissProt Q22639 EMBL-EBI
WormBase CE31365 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:16216_AT expressed protein at
ATH1-121501:254584_AT expressed protein at
CANINE:1596451_AT similar to vacuolar protein sorting 54 isoform 2 cfa
CANINE_2:CFA.9055.1.S1_AT similar to vacuolar protein sorting 54 isoform 2 cfa
CANINE_2:CFAAFFX.5690.1.S1_S_AT similar to vacuolar protein sorting 54 isoform 2 cfa
DROSOPHILA_2:1627832_AT scattered dm
DROSGENOME1:154102_AT scattered dm
CHICKEN:GGA.11872.1.S1_S_AT vacuolar protein sorting 54 (yeast) gga
CHICKEN:GGA.14059.1.A1_AT vacuolar protein sorting 54 (yeast) gga
CHICKEN:GGA.1536.1.S1_AT vacuolar protein sorting 54 (yeast) gga
CHICKEN:GGAAFFX.22701.1.S1_S_AT vacuolar protein sorting 54 (yeast) gga
HG-U133_PLUS_2:233656_S_AT vacuolar protein sorting 54 (yeast) hs
HG-U133B:233656_S_AT vacuolar protein sorting 54 (yeast) hs
HU35KSUBC:RC_AA287061_AT vacuolar protein sorting 54 (yeast) hs
HG-U133A:218423_X_AT vacuolar protein sorting 54 (yeast) hs
HG-U133_PLUS_2:218423_X_AT vacuolar protein sorting 54 (yeast) hs
HG-FOCUS:218423_X_AT vacuolar protein sorting 54 (yeast) hs
HG-U133A_2:218423_X_AT vacuolar protein sorting 54 (yeast) hs
U133_X3P:HS.48499.1.S1_3P_A_AT vacuolar protein sorting 54 (yeast) hs
U133_X3P:HS.48499.0.S2_3P_AT vacuolar protein sorting 54 (yeast) hs
HG-U133_PLUS_2:222627_AT vacuolar protein sorting 54 (yeast) hs
HG-U133B:222627_AT vacuolar protein sorting 54 (yeast) hs
HG-U95B:45655_AT vacuolar protein sorting 54 (yeast) hs
HG-U95E:90731_AT vacuolar protein sorting 54 (yeast) hs
HG-U133_PLUS_2:234136_AT Vacuolar protein sorting 54 (yeast) hs
HG-U133B:234136_AT Vacuolar protein sorting 54 (yeast) hs
MOUSE430_2:1442699_AT vacuolar protein sorting 54 (yeast) mm
MOE430B:1442699_AT vacuolar protein sorting 54 (yeast) mm
MU11KSUBA:AA178689_S_AT vacuolar protein sorting 54 (yeast) mm
MG-U74AV2:102670_AT vacuolar protein sorting 54 (yeast) mm
MOE430A:1449095_AT vacuolar protein sorting 54 (yeast) mm
MOUSE430A_2:1449095_AT vacuolar protein sorting 54 (yeast) mm
MOUSE430_2:1449095_AT vacuolar protein sorting 54 (yeast) mm
MOE430A:1418479_AT vacuolar protein sorting 54 (yeast) mm
MOUSE430A_2:1418479_AT vacuolar protein sorting 54 (yeast) mm
MOUSE430_2:1418479_AT vacuolar protein sorting 54 (yeast) mm
MOE430B:1439943_AT vacuolar protein sorting 54 (yeast) mm
MOUSE430_2:1439943_AT vacuolar protein sorting 54 (yeast) mm
MOE430B:1456810_AT vacuolar protein sorting 54 (yeast) mm
MOUSE430_2:1456810_AT vacuolar protein sorting 54 (yeast) mm
MG-U74BV2:112502_AT vacuolar protein sorting 54 (yeast) mm
MU19KSUBA:TC19292_AT Vacuolar protein sorting 54 (yeast), mRNA (cDNA clone MGC:32446 IMAGE:5042879) mm
MU19KSUBA:TC19292_G_AT Vacuolar protein sorting 54 (yeast), mRNA (cDNA clone MGC:32446 IMAGE:5042879) mm
MU19KSUBC:TC35064_AT Vacuolar protein sorting 54 (yeast), mRNA (cDNA clone MGC:32446 IMAGE:5042879) mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6118 electron transport inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5489 electron transporter activity inferred from electronic annotation QuickGO AmiGO
5507 copper ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA97331 Hypothetical protein T21C9.2 [Caenorhabditis elegans] ref|NP_505711.2| related to yeast Vacuolar Protein Sorting factor family member (vps-54) [Caenorhabditis elegans] sp|Q22639|VPS54_CAEEL Vacuolar protein sorting protein 0.0
blast Q61JT8 Vacuolar protein sorting protein 54 emb|CAE64847.1| Hypothetical protein CBG09643 [Caenorhabditis briggsae] 0.0
blast EAA12219 ENSANGP00000019579 [Anopheles gambiae str. PEST] ref|XP_317102.2| ENSANGP00000019579 [Anopheles gambiae str. PEST] 1.0E-103
blast EAA12219 ENSANGP00000019579 [Anopheles gambiae str. PEST] ref|XP_317102.2| ENSANGP00000019579 [Anopheles gambiae str. PEST] 1.0E-46
Sequence
Target Sequence 
>C. ELEGANS:190310_S_AT
tgcaggtgccctacaattggttggattaaagactatatctgttcgaaatttaggtattgc
tctaaagttttacccactcgcaggtcgatcactcgagttagtatgccgcttcattccgat
ggttcatgatgagatggacagagttcttcctgaaaatcgaaaaagtctgcttcggtactt
caagcaggttgaaagtgaataccgcgatcacgtcaacgaaattgctgccaaattaataag
tgtaatagctcattatacaacaaattgtcttggaatgtgggatgtgaaaggagtgattcc
atcgccagaatttcaacaaatttgtcgccatatgctgaaattccacaatggactggttgg
catcatgccaagagatcagatcgaggcgttgttccgtcaagtacacgaaaactttaaagc
caacttacgagaacacgtcactggaatgggtatcacacctcatgacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCAGGTGCCCTACAATTGGTTGGA 634 575 2628 Antisense
CACTCGCAGGTCGATCACTCGAGTT 484 197 2702 Antisense
TCGAGTTAGTATGCCGCTTCATTCC 464 601 2720 Antisense
AAAAGTCTGCTTCGGTACTTCAAGC 597 131 2788 Antisense
GAATACCGCGATCACGTCAACGAAA 675 325 2824 Antisense
GGAGTGATTCCATCGCCAGAATTTC 120 517 2917 Antisense
TTGTCGCCATATGCTGAAATTCCAC 334 707 2949 Antisense
CAATGGACTGGTTGGCATCATGCCA 584 181 2973 Antisense
GATCAGATCGAGGCGTTGTTCCGTC 197 421 3001 Antisense
GGCGTTGTTCCGTCAAGTACACGAA 265 513 3012 Antisense
GGAATGGGTATCACACCTCATGACC 356 531 3070 Antisense
Sequence Source Affymetrix Proprietary Database