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[192939_at] Zinc finger, C3HC4 type (RING finger)

Description F55A11.3 /REP_DB=WormBase Gene ID /WP=CE05945 /TR=Q20798 /GB=CAA96657.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Zinc finger, C3HC4 type (RING finger)
Cluster 6grp_highest_10_10 > 72      6grp_high1_10_10 > 38      4grp_highest_8_8 > 14      4grp_high_8_8 > 14      6grp_highest_nonorm > 75      6grp_total > 09      4grp_total > 09      6grp_highest_sub > Cu      6grp_high1_sub > Cu      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 590
1 2 3 4 range
A 566
(-3)
P 		708.1
(-1.4)
P 		739.1
(-1.1)
P 		1100.8
(3)
P 		535
B 615
(-3)
P 		613.3
(-3)
P 		666.9
(-2.4)
P 		1136.1
(3)
P 		523
C 545.8
(-3)
P 		711.2
(-1.1)
P 		612.2
(-2.2)
P 		1059.2
(3)
P 		513
avr 575.6
(-3) 		677.5
(-1.8) 		672.7
(-1.9) 		1098.7
(3) 		523

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 311
1 2 3 4 5 6 range
A 993.2
(3)
P 		750.1
(-2.2)
P 		714.4
(-3)
P 		774.9
(-1.7)
P 		827.1
(-0.6)
P 		923.8
(1.5)
P 		279
B 1025.6
(3)
P 		746.8
(-2.9)
P 		925.6
(0.9)
P 		842
(-0.9)
P 		742.3
(-3)
P 		805.9
(-1.7)
P 		283
C 880.9
(3)
P 		823
(-0.2)
P 		836.1
(0.5)
P 		773.4
(-3)
P 		836.3
(0.5)
P 		810.9
(-0.9)
P 		108
avr 966.6
(3) 		773.3
(-3) 		825.4
(-1.4) 		796.8
(-2.3) 		801.9
(-2.1) 		846.9
(-0.7) 		193
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 91
1 2 3 4 range
A 206.1
(3)
P 		153.7
(-3)
P 		193.2
(1.5)
P 		161.1
(-2.2)
P 		52
B 196.1
(-0)
P 		151.5
(-3)
P 		154.5
(-2.8)
P 		242.1
(3)
P 		91
C 180.7
(-2.6)
P 		204.5
(1.5)
P 		213.4
(3)
P 		178.6
(-3)
P 		35
avr 194.3
(3) 		169.9
(-3) 		187
(1.2) 		193.9
(2.9) 		24

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 201
1 2 3 4 5 6 range
A 183.1
(-1.5)
P 		266.8
(3)
P 		155.6
(-3)
P 		196.5
(-0.8)
P 		249.6
(2.1)
P 		224.9
(0.7)
P 		111
B 356.8
(3)
P 		248.6
(-1.9)
P 		224.8
(-2.9)
P 		223
(-3)
P 		301.6
(0.5)
P 		300.5
(0.5)
P 		134
C 326.5
(3)
P 		251.1
(0.4)
P 		212.8
(-1)
P 		155.5
(-3)
P 		270.6
(1)
P 		271.5
(1.1)
P 		171
avr 288.8
(3) 		255.5
(0.9) 		197.7
(-2.6) 		191.7
(-3) 		273.9
(2.1) 		265.6
(1.6) 		97
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192939_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12902
Sequence Type Exemplar sequence
Representative Public ID F55A11.3 NCBI
Target Description F55A11.3 /REP_DB=WormBase Gene ID /WP=CE05945 /TR=Q20798 /GB=CAA96657.1 /SUBMIT=HINXTON /CHR=5 /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_073568(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073568 NCBI Caenorhabditis elegans F55A11.3 (F55A11.3) mRNA, complete cds. 11/11 None
SNAP00000030955 ENSEMBL cdna:SNAP chromosome:CEL140:V:11769933:11772256:1 11/11 None
GENEFINDER00000030966 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11767508:11772256:1 11/11 None
F55A11.3.2 ENSEMBL cdna:known chromosome:CEL140:V:11769915:11772474:1 gene:F55A11.3 11/11 A 
F55A11.3.1 ENSEMBL cdna:known chromosome:CEL140:V:11769916:11772600:1 gene:F55A11.3 11/11 A 
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:11769932-11772256(+) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C3HC4 type (RING finger)
Ensembl F55A11.3
Entrez Gene 179612 Entrez gene
SwissProt Q20798 EMBL-EBI
WormBase CE05945 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:258328_AT zinc finger (C3HC4-type RING finger) family protein at
CANINE:1604075_AT similar to synoviolin 1 isoform a cfa
CANINE_2:CFA.17243.1.S1_S_AT similar to synoviolin 1 isoform a cfa
CANINE_2:CFAAFFX.21482.1.S1_S_AT similar to synoviolin 1 isoform a cfa
DROSOPHILA_2:1640897_AT septin interacting protein 3 dm
DROSGENOME1:152352_AT septin interacting protein 3 dm
U133_X3P:HS.75859.1.A1_3P_AT synovial apoptosis inhibitor 1, synoviolin hs
HG-U133_PLUS_2:225090_AT synovial apoptosis inhibitor 1, synoviolin hs
HG-U133B:225090_AT synovial apoptosis inhibitor 1, synoviolin hs
HG-U95E:78756_AT synovial apoptosis inhibitor 1, synoviolin hs
HG-U133_PLUS_2:244522_AT Synovial apoptosis inhibitor 1, synoviolin hs
HG-U133B:244522_AT Synovial apoptosis inhibitor 1, synoviolin hs
HG-U95E:67627_AT Synovial apoptosis inhibitor 1, synoviolin hs
U133_X3P:HS.187033.0.A1_3P_AT Synovial apoptosis inhibitor 1, synoviolin hs
MOE430A:1428070_AT synovial apoptosis inhibitor 1, synoviolin mm
MOUSE430A_2:1428070_AT synovial apoptosis inhibitor 1, synoviolin mm
MOUSE430_2:1428070_AT synovial apoptosis inhibitor 1, synoviolin mm
MOE430B:1443609_S_AT synovial apoptosis inhibitor 1, synoviolin mm
MOUSE430_2:1443609_S_AT synovial apoptosis inhibitor 1, synoviolin mm
MU19KSUBA:TC15340_AT Synovial apoptosis inhibitor 1, synoviolin (Syvn1), mRNA mm
MU19KSUBA:TC15340_G_AT Synovial apoptosis inhibitor 1, synoviolin (Syvn1), mRNA mm
RG-U34B:RC_AA946430_AT similar to HRD1 protein; synoviolin 1 (predicted) rn
RG-U34C:RC_AA858449_AT similar to HRD1 protein; synoviolin 1 (predicted) rn
RAE230A:1371827_AT similar to HRD1 protein; synoviolin 1 (predicted) rn
RAT230_2:1371827_AT similar to HRD1 protein; synoviolin 1 (predicted) rn
RAE230B:1385306_AT Similar to HRD1 protein; synoviolin 1 (predicted) rn
RAT230_2:1385306_AT Similar to HRD1 protein; synoviolin 1 (predicted) rn
RG-U34A:RC_AA893327_I_AT Similar to HRD1 protein; synoviolin 1 (predicted) rn
RG-U34A:RC_AA893327_S_AT Similar to HRD1 protein; synoviolin 1 (predicted) rn
RG-U34B:RC_AI008572_AT Similar to HRD1 protein; synoviolin 1 (predicted) rn
Protein Similarities
Method ID Description E-Value
blast CAA96657 Hypothetical protein F55A11.3 [Caenorhabditis elegans] ref|NP_505969.1| F55A11.3 [Caenorhabditis elegans] 0.0
blast CAE75301 Hypothetical protein CBG23271 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.5.MarR-like transcriptional regulators All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; MarR-like transcriptional regulators 2.20000004768372
Pfam IPR001841 EMBL-EBI Zn-finger, RING 3.9E-15
Pfam IPR006011 EMBL-EBI Syntaxin, N-terminal 2.8E-17
Pfam IPR000727 EMBL-EBI Target SNARE coiled-coil domain 3.1E-18
Pfam IPR001841 EMBL-EBI Zn-finger, RING 3.9E-15
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505969.1 6 5-27,40-62,102-121,142-164,169-191,212-234
F55A11.3.2 6 5-27,40-62,102-121,142-164,169-191,212-234
F55A11.3.1 6 5-27,40-62,102-121,142-164,169-191,212-234
SNAP00000030955 6 5-27,40-62,102-121,142-164,169-191,212-234
GENEFINDER00000030966 6 385-407,420-442,482-501,522-544,549-571,592-614
Sequence
Target Sequence 
>C. ELEGANS:192939_AT
atcaaatattctatgcaccggctccagctaatcgtccagaattcatgaatcttattccac
cgccaccacttccaatggctggaccacctggaatgttcccgatgatgcctccaccaccac
taccacaggttaatacaacacaaggaacttctagtgaaactccaccagtcaacccatctt
actcacaactttccactgaagagcttcgtcgaatggaaggcgagtcgagagaagcgcttc
tggcacgtcttcaagcaatggacaacattatggttcttctcgagtccgcacaaatgcaaa
tgattcaattggcaacggttactccgatccgtcctcgtccagttgtccctagtgatgaat
cagaacaagaagctcccggaccgtcaacagatcaagtcacttcggaagaacaagaaatac
cagcaacatcttcagcaccttctatcttccgtactgaatct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATCAAATATTCTATGCACCGGCTCC 570 27 1238 Antisense
TTCATGAATCTTATTCCACCGCCAC 241 689 1279 Antisense
TGGAATGTTCCCGATGATGCCTCCA 367 547 1326 Antisense
ATCTTACTCACAACTTTCCACTGAA 542 31 1413 Antisense
CTTCTGGCACGTCTTCAAGCAATGG 530 219 1474 Antisense
TTCTTCTCGAGTCCGCACAAATGCA 689 689 1511 Antisense
AATTGGCAACGGTTACTCCGATCCG 391 173 1544 Antisense
TCGTCCAGTTGTCCCTAGTGATGAA 91 605 1572 Antisense
CTCCCGGACCGTCAACAGATCAAGT 602 231 1610 Antisense
AATACCAGCAACATCTTCAGCACCT 245 173 1653 Antisense
ACCTTCTATCTTCCGTACTGAATCT 517 87 1674 Antisense
Sequence Source Affymetrix Proprietary Database