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[172909_x_at] Zinc finger, C3HC4 type (RING finger)

Description C36A4.8 /REP_DB=WormBase Gene ID /WP=CE20540 /TR=Q93335 /GB=CAA91275.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Zinc finger, C3HC4 type (RING finger)
Cluster 6grp_highest_10_10 > 89      6grp_high1_10_10 > 99      4grp_highest_8_8 > 07      4grp_high_8_8 > 13      6grp_highest_nonorm > 90      6grp_total > 99      4grp_total > 11      6grp_highest_sub > In      6grp_cgc > 79      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 200
1 2 3 4 range
A 131.4
(1.1)
P 		121.6
(-0.2)
P 		100
(-3)
P 		145.9
(3)
P 		46
B 160.7
(-3)
P 		163
(-2.9)
P 		161.8
(-2.9)
P 		257.9
(3)
P 		97
C 147.8
(-2.9)
P 		199.1
(-0.9)
P 		146.1
(-3)
P 		300.1
(3)
P 		154
avr 146.6
(-2.4) 		161.2
(-1.5) 		136
(-3) 		234.6
(3) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 145
1 2 3 4 5 6 range
A 129.7
(-2.8)
P 		127.2
(-3)
P 		181.2
(2.3)
P 		147.1
(-1)
P 		188
(3)
P 		154
(-0.4)
P 		61
B 139.6
(-2.3)
P 		163.6
(-1.2)
P 		122.9
(-3)
P 		159.8
(-1.4)
P 		231.1
(1.8)
P 		258.5
(3)
P 		136
C 144.2
(-1.4)
P 		175
(0.2)
P 		113.7
(-3)
P 		115.3
(-2.9)
P 		187.2
(0.8)
P 		228.7
(3)
P 		115
avr 137.8
(-3) 		155.3
(-1.6) 		139.3
(-2.9) 		140.7
(-2.8) 		202.1
(2.1) 		213.7
(3) 		76
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 36
1 2 3 4 range
A 47.9
(3)
P 		26.4
(-1.9)
P 		26.1
(-1.9)
P 		21.4
(-3)
P 		27
B 51.2
(1.7)
P 		40.2
(-2.1)
P 		37.5
(-3)
P 		55
(3)
P 		18
C 48.9
(-3)
P 		57.2
(3)
P 		50.9
(-1.6)
P 		50.6
(-1.8)
P 		8
avr 49.3
(3) 		41.3
(-1.3) 		38.2
(-3) 		42.3
(-0.8) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 73
1 2 3 4 5 6 range
A 23.9
(-3)
P 		45.2
(0.9)
P 		39.5
(-0.1)
P 		37.3
(-0.5)
P 		56.7
(3)
P 		37.5
(-0.5)
P 		33
B 48.6
(-1.3)
P 		54.5
(-0.8)
P 		29.8
(-3)
P 		42.3
(-1.9)
P 		93.9
(2.8)
P 		96.4
(3)
P 		67
C 53.5
(0.4)
P 		53.4
(0.4)
P 		28.9
(-2.4)
P 		23.2
(-3)
P 		60.6
(1.2)
P 		76.6
(3)
P 		53
avr 42
(-1.5) 		51
(-0.1) 		32.7
(-3) 		34.3
(-2.7) 		70.4
(3) 		70.2
(3) 		38
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172909_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6215
Sequence Type Exemplar sequence
Representative Public ID C36A4.8 NCBI
Target Description C36A4.8 /REP_DB=WormBase Gene ID /WP=CE20540 /TR=Q93335 /GB=CAA91275.1 /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 Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_065379
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065379 NCBI Caenorhabditis elegans BRCa homolog (tumor suppressor gene Brca1) family member (brc-1) (brc-1) mRNA, complete cds. A 
GENEFINDER00000028402 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:3858283:3862935:-1 None
SNAP00000028398 ENSEMBL cdna:SNAP chromosome:CEL140:III:3858283:3862935:-1 None
C36A4.8 ENSEMBL cdna:known chromosome:CEL140:III:3853121:3862935:-1 gene:C36A4.8 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_062063 1/11 Cross Hyb Matching Probes A 
NM_060750 1/11 Cross Hyb Matching Probes A 
NM_067922 2/11 Cross Hyb Matching Probes A 
GENEFINDER00000031055 1/11 Cross Hyb Matching Probes None
SNAP00000028397 4/11 Cross Hyb Matching Probes None
GENEFINDER00000023868 1/11 Cross Hyb Matching Probes None
SNAP00000037843 2/11 Cross Hyb Matching Probes None
GENEFINDER00000037856 2/11 Cross Hyb Matching Probes None
E03H4.8 1/11 Cross Hyb Matching Probes A 
Y27F2A.5 1/11 Cross Hyb Matching Probes A 
M142.7 1/11 Cross Hyb Matching Probes None
W05B2.3 2/11 Cross Hyb Matching Probes None
F42A6.5 2/11 Cross Hyb Matching Probes A 
T07C12.5 2/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:3853214-3862935(-) 88.67 100.0
Public Domain and Genome References
Gene Title Zinc finger, C3HC4 type (RING finger)
Gene Symbol brc-1
Ensembl C36A4.8
Entrez Gene 175499 Entrez gene
SwissProt Q93335 EMBL-EBI
WormBase CE31438 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA91275 Hypothetical protein C36A4.8 [Caenorhabditis elegans] ref|NP_497780.2| BRCa homolog (tumor suppressor gene Brca1) family member (brc-1) [Caenorhabditis elegans] 0.0
blast AAC68936 Hypothetical protein T12B5.6 [Caenorhabditis elegans] ref|NP_497296.1| T12B5.6 [Caenorhabditis elegans] 0.0
blast T32726 hypothetical protein C45H4.5 - Caenorhabditis elegans 0.0
blast T18779 transposase containing protein - Caenorhabditis elegans 0.0
blast CAE60090 Hypothetical protein CBG03614 [Caenorhabditis briggsae] 1.0E-107
Protein Domains
Database ID Description E-Value
Pfam IPR001888 EMBL-EBI Transposase, type 1 2.8E-41
Pfam IPR001841 EMBL-EBI Zn-finger, RING 3.3E-11
Pfam IPR001357 EMBL-EBI BRCT 0.23
Pfam IPR001357 EMBL-EBI BRCT 3.0E-5
Sequence
Target Sequence 
>C. ELEGANS:172909_X_AT
aagccagtggtcgtagcatcagatgatgatgaagttgtagaagattctgaaggagaacta
caaattgatgaagatgatctggcaaatgttacctgtgctacaagtgtaagaaatatagga
aaatcattgtgtgcagaatatatcaggggtgtgcggcaaatttgccgaatttgtcgtttg
ccgagctcggcaaatttcaaaaaagttgatttgccgaatttgccgagctcggcaaatttc
gaaatttgccgcacacgtcaaaaatttgacagtacaatttcgactaaaactactgatttt
ttcgccaaaaattcacaactaatcgagcttgtccaacaatgcggaggagaaattctgagt
tgctacgagaatctgtcacctgaaaaactctacataatcttctcaaaacactcaaaagca
attgaagaatcaaaaaatatcgagaatctgtataaatgtgatgtggtgacaatggaatgg
gtattggacagtatcagtgaatatttaattctacccactcaac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGCCAGTGGTCGTAGCATCAGATG 42 149 967 Antisense
GGCAAATGTTACCTGTGCTACAAGT 284 535 1047 Antisense
ATCAGGGGTGTGCGGCAAATTTGCC 481 1 1108 Antisense
TGCCGAATTTGTCGTTTGCCGAGCT 396 585 1129 Antisense
TTGATTTGCCGAATTTGCCGAGCTC 620 703 1172 Antisense
GCCGAGCTCGGCAAATTTCGAAATT 301 283 1188 Antisense
TTTCGAAATTTGCCGCACACGTCAA 593 669 1203 Antisense
AATCGAGCTTGTCCAACAATGCGGA 556 167 1287 Antisense
GTTGCTACGAGAATCTGTCACCTGA 610 439 1325 Antisense
AAAACTCTACATAATCTTCTCAAAA 371 131 1350 Antisense
GAATATTTAATTCTACCCACTCAAC 560 321 1465 Antisense
Sequence Source Affymetrix Proprietary Database