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[193619_at] Zinc finger, C3HC4 type (RING finger)

Description F45G2.6 /REP_DB=WormBase Gene ID /WP=CE16049 /GEN=trf-1 /TR=O62248 /GB=CAB07615.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Zinc finger, C3HC4 type (RING finger)
Cluster 6grp_high1_10_10 > 01      6grp_total > 19      4grp_total > 36      6grp_cgc > 90      6grp_high1_sub > De      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 84
1 2 3 4 range
A 103.4
(2.6)
P 		108
(3)
P 		91.3
(1.5)
A 		40
(-3)
A 		68
B 104.9
(1.1)
P 		124.2
(3)
P 		62.6
(-3)
A 		95.1
(0.2)
A 		62
C 69.7
(-1)
P 		107.8
(3)
P 		50.7
(-3)
P 		103.6
(2.6)
M 		57
avr 92.7
(0.3) 		113.3
(3) 		68.2
(-3) 		79.6
(-1.5) 		45

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 81
1 2 3 4 5 6 range
A 92.4
(0.2)
A 		56.5
(-3)
A 		68.9
(-1.9)
A 		90.6
(0.1)
P 		122.8
(3)
A 		86.8
(-0.3)
P 		66
B 133.9
(3)
P 		65.6
(-2.2)
P 		115.3
(1.6)
P 		55.8
(-3)
A 		101.6
(0.5)
P 		76
(-1.4)
P 		78
C 90.4
(0.9)
P 		105.6
(2.4)
P 		109.2
(2.8)
A 		111
(3)
A 		73.7
(-0.9)
P 		53
(-3)
P 		58
avr 105.6
(3) 		75.9
(-2.3) 		97.8
(1.6) 		85.8
(-0.5) 		99.4
(1.9) 		71.9
(-3) 		34
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 32
1 2 3 4 range
A 37.7
(3)
P 		23.4
(0.3)
P 		23.9
(0.4)
A 		5.9
(-3)
A 		32
B 33.5
(3)
P 		30.7
(2.1)
P 		14.5
(-3)
A 		20.3
(-1.2)
A 		19
C 23.1
(-0.5)
P 		31
(3)
P 		17.7
(-2.9)
P 		17.5
(-3)
M 		14
avr 31.4
(3) 		28.4
(1.9) 		18.7
(-1.5) 		14.6
(-3) 		17

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 32
1 2 3 4 5 6 range
A 17
(-2.5)
A 		20.1
(-1.6)
A 		15
(-3)
A 		23
(-0.8)
P 		37.1
(3)
A 		21.1
(-1.3)
P 		22
B 46.6
(3)
P 		21.8
(-1.7)
P 		28
(-0.5)
P 		14.8
(-3)
A 		41.3
(2)
P 		28.4
(-0.4)
P 		32
C 33.5
(3)
P 		32.2
(2.5)
P 		27.8
(0.8)
A 		22.3
(-1.3)
A 		23.8
(-0.7)
P 		17.8
(-3)
P 		16
avr 32.4
(2.3) 		24.7
(-1) 		23.6
(-1.5) 		20
(-3) 		34.1
(3) 		22.4
(-2) 		14
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193619_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7537
Sequence Type Exemplar sequence
Representative Public ID F45G2.6 NCBI
Target Description F45G2.6 /REP_DB=WormBase Gene ID /WP=CE16049 /GEN=trf-1 /TR=O62248 /GB=CAB07615.1 /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_067372(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067372 NCBI Caenorhabditis elegans TNF Receptor Associated Factor (TRAF) homolog family member (trf-1) (trf-1) mRNA, complete cds. 11/11 None
SNAP00000011671 ENSEMBL cdna:SNAP chromosome:CEL140:III:13429977:13432910:1 11/11 None
GENEFINDER00000011685 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13429977:13432910:1 11/11 None
F45G2.6 ENSEMBL cdna:known chromosome:CEL140:III:13429978:13432910:1 gene:F45G2.6 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
chrIII:13429972-13432906(+) 100.0 100.0
Public Domain and Genome References
Gene Title Zinc finger, C3HC4 type (RING finger)
Gene Symbol trf-1
Ensembl F45G2.6
Entrez Gene 176767 Entrez gene
SwissProt O62248 EMBL-EBI
WormBase CE37519 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1627704_A_AT TNF-receptor-associated factor 1 dm
DROSGENOME1:153984_AT TNF-receptor-associated factor 1 dm
CHICKEN:GGAAFFX.2480.1.S1_AT similar to TRAF4 protein gga
HG-U133A:202871_AT TNF receptor-associated factor 4 hs
HG-U133_PLUS_2:202871_AT TNF receptor-associated factor 4 hs
HG-U133A_2:202871_AT TNF receptor-associated factor 4 hs
HG-FOCUS:202871_AT TNF receptor-associated factor 4 hs
HG-U133_PLUS_2:211899_S_AT TNF receptor-associated factor 4 hs
HG-U133A:211899_S_AT TNF receptor-associated factor 4 hs
HG-U133A_2:211899_S_AT TNF receptor-associated factor 4 hs
HUGENEFL:X80200_AT TNF receptor-associated factor 4 hs
U133_X3P:G4759251_3P_AT TNF receptor-associated factor 4 hs
U133_X3P:G3435255_3P_A_AT TNF receptor-associated factor 4 hs
U133_X3P:HS.35437.1.A1_3P_AT TNF receptor-associated factor 4 hs
U133_X3P:HS.35437.1.A1_3P_A_AT TNF receptor-associated factor 4 hs
HG-U133_PLUS_2:242473_AT TNF receptor-associated factor 4 hs
HG-U133B:242473_AT TNF receptor-associated factor 4 hs
HG-U95AV2:37912_AT TNF receptor-associated factor 4 hs
HG-U133_PLUS_2:235688_S_AT TNF receptor-associated factor 4 hs
HG-U133B:235688_S_AT TNF receptor-associated factor 4 hs
HG-U95B:45941_AT TNF receptor-associated factor 4 hs
HU35KSUBB:RC_R95689_AT TNF receptor-associated factor 4 hs
U133_X3P:HS.35437.0.A1_3P_A_AT TNF receptor-associated factor 4 hs
MU11KSUBB:X92346_S_AT Tnf receptor associated factor 4 mm
MG-U74AV2:100005_AT Tnf receptor associated factor 4 mm
MG-U74CV2:167379_AT Tnf receptor associated factor 4 mm
MOE430A:1460642_AT Tnf receptor associated factor 4 mm
MOUSE430A_2:1460642_AT Tnf receptor associated factor 4 mm
MOUSE430_2:1460642_AT Tnf receptor associated factor 4 mm
MOE430A:1416571_AT Tnf receptor associated factor 4 mm
MOUSE430A_2:1416571_AT Tnf receptor associated factor 4 mm
MOUSE430_2:1416571_AT Tnf receptor associated factor 4 mm
MOE430B:1440892_AT TNF receptor associated factor 4 (traf4) mm
MOUSE430_2:1440892_AT TNF receptor associated factor 4 (traf4) mm
RAE230A:1371551_AT Tnf receptor associated factor 4 (predicted) rn
RAT230_2:1371551_AT Tnf receptor associated factor 4 (predicted) rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB07615 Hypothetical protein F45G2.6 [Caenorhabditis elegans] ref|NP_499773.2| TNF Receptor Associated Factor (TRAF) homolog family member (trf-1) [Caenorhabditis elegans] gb|AAK37546.1| TRF-1 [Caenorhabditis elegans] 0.0
blast CAE73706 Hypothetical protein CBG21219 [Caenorhabditis briggsae] 0.0
blast XP_780297 PREDICTED: similar to TNF Receptor associated Factor homolog (52.4 kD) (trf-1) [Strongylocentrotus purpuratus] 5.0E-68
Protein Domains
Database ID Description E-Value
Pfam IPR002083 EMBL-EBI MATH 8.2E-25
Pfam IPR001293 EMBL-EBI Zn-finger, TRAF type 1.1E-26
Pfam IPR002083 EMBL-EBI MATH 8.2E-25
Pfam IPR001293 EMBL-EBI Zn-finger, TRAF type 1.1E-26
Pfam IPR002083 EMBL-EBI MATH 8.2E-25
Pfam IPR001293 EMBL-EBI Zn-finger, TRAF type 1.1E-26
Sequence
Target Sequence 
>C. ELEGANS:193619_AT
gagatgttcggtcctcaactgatatggaaaatcgataagcttcaacaaagaactaatgag
gcgaagtccggagccgacacgaccattttctcggtgcccttcatgtctcatcgatttggt
tataagatgatggcttgtgcatgtcttttcggtgatggatcaagcgctggaaagtcaatc
tccttgtacgtgttgttgctcaaaggagagttcgatccaacactcgaatggccatttcat
cgagcaatcaagatatctctgttggatcagaacccgcgtcccgaagatcgtgtaaacatc
acttatgtcattgatcctcgaaaactgaaagccaatgagaagttcttggctcgtccacgt
ggtgaacgtaatgctgcttttggatctcagtccttctgctcattggctatattgcagaat
tatgtgaaggacgacaaaatctacgttcaaatcgacgtggatcgctgtgagacccttcca
gttcagcttaagagtcgtgatgcaaaagaacgaaagcaaatgctcgatgcaatgcgtgca
aagactccagatgttcgccttcatcaagttcgtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGATGTTCGGTCCTCAACTGATAT 668 395 928 Antisense
CCCTTCATGTCTCATCGATTTGGTT 539 259 1024 Antisense
TGATGGCTTGTGCATGTCTTTTCGG 405 567 1055 Antisense
GTCAATCTCCTTGTACGTGTTGTTG 389 463 1101 Antisense
AATGAGAAGTTCTTGGCTCGTCCAC 328 165 1261 Antisense
ATGCTGCTTTTGGATCTCAGTCCTT 688 41 1298 Antisense
AGTCCTTCTGCTCATTGGCTATATT 434 59 1316 Antisense
ATCGACGTGGATCGCTGTGAGACCC 149 35 1378 Antisense
GACCCTTCCAGTTCAGCTTAAGAGT 621 381 1398 Antisense
GTGCAAAGACTCCAGATGTTCGCCT 563 479 1463 Antisense
GATGTTCGCCTTCATCAAGTTCGTC 560 409 1477 Antisense
Sequence Source Affymetrix Proprietary Database