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[193778_s_at] Zinc finger, C3HC4 type (RING finger)

Description C16C10.7 /REP_DB=WormBase Gene ID /WP=CE01498 /GEN=rnf-5 /TR=SW:Q09463 /GB=CAA86745.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Zinc finger, C3HC4 type (RING finger)
Cluster 6grp_highest_10_10 > 98      6grp_high1_10_10 > 93      4grp_highest_8_8 > 42      4grp_high_8_8 > 41      6grp_highest_nonorm > 85      6grp_total > 95      4grp_total > 54      6grp_highest_sub > Cu      6grp_cgc > 77      6grp_high1_sub > 04      6grp_cgc_sub > 04_05_06      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 328
1 2 3 4 range
A 893.5
(3)
P 		648.1
(-2.2)
P 		693.1
(-1.3)
P 		611.6
(-3)
P 		282
B 923.9
(3)
P 		701.6
(-1.1)
P 		738.3
(-0.4)
P 		597.4
(-3)
P 		327
C 923.3
(3)
P 		754.5
(-0.1)
P 		705.7
(-1)
P 		596.4
(-3)
P 		327
avr 913.6
(3) 		701.4
(-1.1) 		712.4
(-0.9) 		601.8
(-3) 		312

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 390
1 2 3 4 5 6 range
A 920.7
(2.3)
P 		660.1
(-3)
P 		781
(-0.6)
P 		956.5
(3)
P 		801.6
(-0.1)
P 		814.9
(0.1)
P 		296
B 746.4
(-1.6)
P 		739.6
(-1.7)
P 		690.4
(-3)
P 		894.9
(2.2)
P 		924.5
(3)
P 		820.7
(0.3)
P 		234
C 853
(-0.8)
P 		756.3
(-2.7)
P 		739.2
(-3)
P 		815.4
(-1.5)
P 		811.7
(-1.6)
P 		1050.2
(3)
P 		311
avr 840
(1.1) 		718.7
(-3) 		736.9
(-2.4) 		888.9
(2.8) 		845.9
(1.3) 		895.3
(3) 		177
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 236
1 2 3 4 range
A 325.3
(3)
P 		140.7
(-1.7)
P 		181.2
(-0.7)
P 		89.5
(-3)
P 		236
B 294.6
(3)
P 		173.3
(-1.4)
P 		171.1
(-1.4)
P 		127.3
(-3)
P 		167
C 305.7
(3)
P 		216.9
(0.4)
P 		246
(1.3)
P 		100.6
(-3)
P 		205
avr 308.5
(3) 		177
(-0.9) 		199.4
(-0.2) 		105.8
(-3) 		203

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 212
1 2 3 4 5 6 range
A 169.7
(-3)
P 		234.8
(2.4)
P 		170.1
(-3)
P 		242.6
(3)
P 		241.9
(2.9)
P 		198.4
(-0.6)
P 		73
B 259.7
(-0.3)
P 		246.2
(-0.7)
P 		167.6
(-3)
P 		237
(-1)
P 		375.6
(3)
P 		306
(1)
P 		208
C 316.2
(1.9)
P 		230.8
(-0.9)
P 		188.1
(-2.2)
P 		164
(-3)
P 		262.6
(0.2)
P 		351.5
(3)
P 		188
avr 248.5
(0.7) 		237.3
(0.1) 		175.3
(-3) 		214.5
(-1) 		293.4
(3) 		285.3
(2.6) 		118
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193778_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7913
Sequence Type Exemplar sequence
Representative Public ID C16C10.7 NCBI
Target Description C16C10.7 /REP_DB=WormBase Gene ID /WP=CE01498 /GEN=rnf-5 /TR=SW:Q09463 /GB=CAA86745.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Zinc finger, C3HC4 type (RING finger)
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_065429(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065429 NCBI Caenorhabditis elegans RiNg Finger protein family member (rnf-5) (rnf-5) mRNA, complete cds. 11/11 None
SNAP00000043772 ENSEMBL cdna:SNAP chromosome:CEL140:III:4164514:4168736:-1 11/11 None
GENEFINDER00000043787 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4164514:4168736:-1 11/11 None
C16C10.7 ENSEMBL cdna:known chromosome:CEL140:III:4164304:4166806:-1 gene:C16C10.7 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
chrIII:4164513-4166804(-) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C3HC4 type (RING finger)
Gene Symbol rnf-5
Ensembl C16C10.7
Entrez Gene 175532 Entrez gene
SwissProt Q09463 EMBL-EBI
WormBase CE01498 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:13330_AT zinc finger (C3HC4-type RING finger) family protein at
ATH1-121501:267297_AT zinc finger (C3HC4-type RING finger) family protein at
CANINE_2:CFA.18316.1.S1_AT similar to ring finger protein 185 cfa
CANINE_2:CFA.18316.1.S1_S_AT similar to ring finger protein 185 cfa
CANINE_2:CFAAFFX.20117.1.S1_AT similar to ring finger protein 185 cfa
CANINE_2:CFAAFFX.20117.1.S1_S_AT similar to ring finger protein 185 cfa
DROSOPHILA_2:1634577_S_AT dm
DROSOPHILA_2:1628101_S_AT dm
DROSGENOME1:152551_AT dm
CHICKEN:GGA.4866.2.S1_AT ring finger protein 185 gga
CHICKEN:GGA.4866.2.S1_S_AT ring finger protein 185 gga
HU35KSUBA:RC_AA258379_AT ring finger protein 185 hs
U133_X3P:HS.279535.1.S1_3P_AT ring finger protein 185 hs
HG-U133_PLUS_2:224750_AT ring finger protein 185 hs
HG-U133B:224750_AT ring finger protein 185 hs
HG-U95B:57146_AT ring finger protein 185 hs
HG-U95AV2:640_AT Ring finger protein 185 hs
HC-G110:640_AT Ring finger protein 185 hs
HG-U133_PLUS_2:207280_AT Ring finger protein 185 hs
HG-U133A:207280_AT Ring finger protein 185 hs
HG-FOCUS:207280_AT Ring finger protein 185 hs
HG-U133A_2:207280_AT Ring finger protein 185 hs
HUGENEFL:L48211_AT Ring finger protein 185 hs
U133_X3P:G6031157_3P_AT Ring finger protein 185 hs
MG-U74BV2:107632_AT ring finger protein 185 mm
MG-U74BV2:164689_I_AT ring finger protein 185 mm
MG-U74CV2:167679_F_AT ring finger protein 185 mm
MOE430A:1451108_AT ring finger protein 185 mm
MOUSE430A_2:1451108_AT ring finger protein 185 mm
MOUSE430_2:1451108_AT ring finger protein 185 mm
MOE430B:1459877_X_AT Ring finger protein 185 (Rnf185), mRNA mm
MOUSE430_2:1459877_X_AT Ring finger protein 185 (Rnf185), mRNA mm
MU19KSUBA:TC19608_AT Ring finger protein 185 (Rnf185), mRNA mm
MU19KSUBA:TC19608_G_AT Ring finger protein 185 (Rnf185), mRNA mm
MU19KSUBB:TC34265_AT Ring finger protein 185 (Rnf185), mRNA mm
RG-U34B:RC_AA943095_AT similar to 1700022N24Rik protein rn
RAE230A:1374701_AT similar to 1700022N24Rik protein rn
RAT230_2:1374701_AT similar to 1700022N24Rik protein rn
Protein Similarities
Method ID Description E-Value
blast CAA86744 Hypothetical protein C16C10.6 [Caenorhabditis elegans] ref|NP_497831.1| C16C10.6 [Caenorhabditis elegans] sp|Q09252|YQ56_CAEEL Hypothetical protein C16C10.6 in chromosome III 1.0E-168
blast CAA86744 Hypothetical protein C16C10.6 [Caenorhabditis elegans] ref|NP_497831.1| C16C10.6 [Caenorhabditis elegans] sp|Q09252|YQ56_CAEEL Hypothetical protein C16C10.6 in chromosome III 1.0E-165
blast CAE72854 Hypothetical protein CBG20153 [Caenorhabditis briggsae] 1.0E-123
blast CAE72854 Hypothetical protein CBG20153 [Caenorhabditis briggsae] 1.0E-121
blast CAA86745 Hypothetical protein C16C10.7 [Caenorhabditis elegans] ref|NP_497830.1| RiNg Finger protein family member (rnf-5) [Caenorhabditis elegans] sp|Q09463|RNF5_CAEEL RING finger protein 1.0E-103
blast CAA86745 Hypothetical protein C16C10.7 [Caenorhabditis elegans] ref|NP_497830.1| RiNg Finger protein family member (rnf-5) [Caenorhabditis elegans] sp|Q09463|RNF5_CAEEL RING finger protein 1.0E-102
blast CAE72853 Hypothetical protein CBG20152 [Caenorhabditis briggsae] 6.0E-84
Protein Domains
Database ID Description E-Value
Pfam IPR001841 EMBL-EBI Zn-finger, RING 3.2E-16
Pfam IPR001841 EMBL-EBI Zn-finger, RING 3.2E-16
Pfam IPR001841 EMBL-EBI Zn-finger, RING 3.2E-16
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_497830.1 2 140-162,217-234
C16C10.7 2 140-162,217-234
SNAP00000043772 2 532-554,609-626
GENEFINDER00000043787 2 568-590,645-662
Sequence
Target Sequence 
>C. ELEGANS:193778_S_AT
gcagtcgtttccctatgtggacatcttttttgttggccatgtctgagtcaatggcttgat
actcgtccaaataatcaagtttgtccagtgtgtaaaagtgcaattgatgggaataaagtt
gtaccgatctatggaagaggtggcgattcatcggatccacgtaaaaaagttccaccacgt
ccaaaaggacaacgaagtgaaccaccaccgcaatcatttgccggtttcaattggggtggc
gatggcggaatgatgggcggcggcggaccaaatgtgcatttttcatttggaattggtacg
gtgaatggtctgttcccgttgatgttcatgctacctttcattcaaggcatcttcccattg
tcatttgttgcttcattctttggaaatggtaatcaaggagcagcagcagctggtggtgga
aatggtggaggaaatgacggaaatgatggtacacatgcacatactcatggacatacacat
ggaccccgtggacacggagaatcagctgcaccgggatcaagaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAGTCGTTTCCCTATGTGGACATC 527 311 118 Antisense
GTCAATGGCTTGATACTCGTCCAAA 471 463 164 Antisense
GAGGTGGCGATTCATCGGATCCACG 394 393 254 Antisense
GGACAACGAAGTGAACCACCACCGC 537 525 304 Antisense
ACCACCGCAATCATTTGCCGGTTTC 115 85 321 Antisense
GGCGATGGCGGAATGATGGGCGGCG 652 541 355 Antisense
CGGTGAATGGTCTGTTCCCGTTGAT 3 243 416 Antisense
TGATGTTCATGCTACCTTTCATTCA 384 565 437 Antisense
TTCATTCAAGGCATCTTCCCATTGT 410 683 454 Antisense
TTCCCATTGTCATTTGTTGCTTCAT 696 697 469 Antisense
GAATCAGCTGCACCGGGATCAAGAA 27 329 616 Antisense
Sequence Source Affymetrix Proprietary Database