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[173744_at]

Description AV194322 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y56A3A.20 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV194322 /WB_GENE_ID=Y56A3A.20 /WP=CE22588 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk628a10 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 90      6grp_high1_10_10 > 19      4grp_highest_8_8 > 01      4grp_high_8_8 > 45      6grp_highest_nonorm > 20      6grp_total > 19      4grp_total > 50      6grp_cgc > 02      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 711
1 2 3 4 range
A 864.3
(-3)
P 		1363.7
(3)
P 		1263.5
(1.8)
P 		952.8
(-1.9)
P 		499
B 931.7
(-1.4)
P 		1202.2
(2.5)
P 		1238
(3)
P 		816.3
(-3)
P 		422
C 1035.5
(-0.9)
P 		1498
(3)
P 		1338.5
(1.7)
P 		787.1
(-3)
P 		711
avr 943.8
(-1.9) 		1354.6
(3) 		1280
(2.1) 		852.1
(-3) 		503

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1069
1 2 3 4 5 6 range
A 1329.6
(2.4)
P 		831.9
(-1.4)
P 		691.3
(-2.5)
P 		720.6
(-2.3)
P 		1414.1
(3)
P 		628.4
(-3)
P 		786
B 1323.2
(3)
P 		1046.8
(0.3)
P 		832.4
(-1.7)
P 		860.5
(-1.4)
P 		1102.9
(0.9)
P 		699.1
(-3)
P 		624
C 1615.3
(3)
P 		733.8
(-1.9)
P 		904
(-1)
P 		808.7
(-1.5)
P 		1260.4
(1)
P 		546.7
(-3)
P 		1069
avr 1422.7
(3) 		870.8
(-1.1) 		809.2
(-1.6) 		796.6
(-1.7) 		1259.1
(1.8) 		624.7
(-3) 		798
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 334
1 2 3 4 range
A 314.7
(2.5)
P 		296
(1.9)
P 		330.3
(3)
P 		139.5
(-3)
P 		191
B 297.1
(3)
P 		296.9
(3)
P 		286.9
(2.5)
P 		173.9
(-3)
P 		123
C 342.8
(0.8)
P 		430.7
(2.4)
P 		466.5
(3)
P 		132.7
(-3)
P 		334
avr 318.2
(1.8) 		341.2
(2.4) 		361.2
(3) 		148.7
(-3) 		213

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 448
1 2 3 4 5 6 range
A 245.1
(-0.9)
P 		295.9
(0.2)
P 		150.6
(-3)
P 		182.8
(-2.3)
P 		426.7
(3)
P 		153
(-2.9)
P 		276
B 460.4
(3)
P 		348.4
(0.4)
P 		202.1
(-3)
P 		227.9
(-2.4)
P 		448.1
(2.7)
P 		260.7
(-1.6)
P 		258
C 598.7
(3)
P 		223.9
(-2.2)
P 		230.1
(-2.1)
P 		162.6
(-3)
P 		407.9
(0.4)
P 		183
(-2.7)
P 		436
avr 434.7
(3) 		289.4
(-0.6) 		194.3
(-2.9) 		191.1
(-3) 		427.6
(2.8) 		198.9
(-2.8) 		244
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173744_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24022
Sequence Type Exemplar sequence
Representative Public ID AV194322 NCBI
Target Description AV194322 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y56A3A.20 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV194322 /WB_GENE_ID=Y56A3A.20 /WP=CE22588 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk628a10 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_067152(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067152 NCBI Caenorhabditis elegans yeast CCR4 Associated Factor family member (ccf-1) (ccf-1) mRNA, complete cds. 11/11 A 
Y56A3A.20.1 ENSEMBL cdna:known chromosome:CEL140:III:11918722:11920113:-1 gene:Y56A3A.20 11/11 None
Y56A3A.20.2 ENSEMBL cdna:known chromosome:CEL140:III:11918747:11920118:-1 gene:Y56A3A.20 11/11 None
Y56A3A.20.3 ENSEMBL cdna:known chromosome:CEL140:III:11918747:11920115:-1 gene:Y56A3A.20 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:11918734-11920093(-) 97.14 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ccf-1
Ensembl Y56A3A.20
Entrez Gene 176625 Entrez gene
SwissProt Q17345 EMBL-EBI
WormBase CE22588 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:19915_AT CCR4-NOT transcription complex protein, putative at
ATH1-121501:265676_AT CCR4-NOT transcription complex protein, putative at
CANINE:1603255_AT similar to CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1) cfa
CANINE_2:CFA.18438.1.S1_S_AT similar to CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1) cfa
CANINE_2:CFAAFFX.11236.1.S1_AT similar to CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1) cfa
DROSOPHILA_2:1634474_S_AT dm
DROSGENOME1:142198_AT dm
CHICKEN:GGA.4905.1.S1_S_AT CCR4-NOT transcription complex, subunit 7 gga
CHICKEN:GGA.4905.2.A1_AT CCR4-NOT transcription complex, subunit 7 gga
HG-U133_PLUS_2:218250_S_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U133A:218250_S_AT CCR4-NOT transcription complex, subunit 7 hs
HG-FOCUS:218250_S_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U133A_2:218250_S_AT CCR4-NOT transcription complex, subunit 7 hs
HU35KSUBA:RC_AA256678_AT CCR4-NOT transcription complex, subunit 7 hs
HU35KSUBA:D82636_AT CCR4-NOT transcription complex, subunit 7 hs
HU35KSUBA:RC_AA282791_AT CCR4-NOT transcription complex, subunit 7 hs
U133_X3P:G10518495_3P_S_AT CCR4-NOT transcription complex, subunit 7 hs
U133_X3P:HS2.380963.2.S1_3P_S_AT CCR4-NOT transcription complex, subunit 7 hs
U133_X3P:HS.226318.1.A2_3P_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U133_PLUS_2:1552344_S_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U133_PLUS_2:225053_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U133B:225053_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U95B:45318_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U95C:65775_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U95E:73366_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U133_PLUS_2:233019_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U133B:233019_AT CCR4-NOT transcription complex, subunit 7 hs
U133_X3P:HS.287574.0.S1_3P_AT CCR4-NOT transcription complex, subunit 7 hs
HG-U95D:67499_AT CCR4-NOT transcription complex, subunit 7 hs
MOUSE430A_2:1460665_A_AT CCR4-NOT transcription complex, subunit 7 mm
MOUSE430_2:1460665_A_AT CCR4-NOT transcription complex, subunit 7 mm
MOE430A:1460665_A_AT CCR4-NOT transcription complex, subunit 7 mm
MOUSE430A_2:1430519_A_AT CCR4-NOT transcription complex, subunit 7 mm
MOE430A:1430519_A_AT CCR4-NOT transcription complex, subunit 7 mm
MOUSE430_2:1430519_A_AT CCR4-NOT transcription complex, subunit 7 mm
MOUSE430_2:1423641_S_AT CCR4-NOT transcription complex, subunit 7 mm
MOE430A:1423641_S_AT CCR4-NOT transcription complex, subunit 7 mm
MOUSE430A_2:1423641_S_AT CCR4-NOT transcription complex, subunit 7 mm
MU11KSUBA:U21855_S_AT CCR4-NOT transcription complex, subunit 7 mm
MG-U74AV2:101564_AT CCR4-NOT transcription complex, subunit 7 mm
MG-U74AV2:162314_AT CCR4-NOT transcription complex, subunit 7 mm
MG-U74AV2:160401_R_AT CCR4-NOT transcription complex, subunit 7 mm
MU19KSUBA:TC21067_AT CCR4-NOT transcription complex, subunit 7, mRNA (cDNA clone MGC:6050 IMAGE:3590764) mm
MU19KSUBA:TC21067_G_AT CCR4-NOT transcription complex, subunit 7, mRNA (cDNA clone MGC:6050 IMAGE:3590764) mm
RG-U34C:RC_AI071980_AT CCR4-NOT transcription complex, subunit 7 (predicted) rn
RG-U34C:RC_AI101934_AT CCR4-NOT transcription complex, subunit 7 (predicted) rn
RAE230A:1367515_AT CCR4-NOT transcription complex, subunit 7 (predicted) rn
RAE230B:1367515_AT CCR4-NOT transcription complex, subunit 7 (predicted) rn
RAT230_2:1367515_AT CCR4-NOT transcription complex, subunit 7 (predicted) rn
RAE230B:1395033_AT CCR4-NOT transcription complex, subunit 7 (predicted) rn
RAT230_2:1395033_AT CCR4-NOT transcription complex, subunit 7 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
16481 negative regulation of transcription inferred from electronic annotation QuickGO AmiGO
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
16564 transcriptional repressor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB60501 Hypothetical protein Y56A3A.20 [Caenorhabditis elegans] ref|NP_499553.1| yeast CCR4 Associated Factor family member (ccf-1) [Caenorhabditis elegans] sp|Q17345|CNOT7_CAEEL CCR4-NOT transcription complex subunit 7 (CCR4-associated factor 1) (CAF1) gb|AAA87454.1| cCAF1 protein [Caenorhabditis elegans] 1.0E-159
blast CAE67745 Hypothetical protein CBG13320 [Caenorhabditis briggsae] emb|CAE67740.1| Hypothetical protein CBG13315 [Caenorhabditis briggsae] 1.0E-146
blast BAE06351.1 Ci-CNOT7/8 [Ciona intestinalis] 1.0E-66
Protein Domains
Database ID Description E-Value
Pfam IPR006941 EMBL-EBI CAF1 family ribonuclease 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:173744_AT
caagcctgaacagatctctttcccgtcatttttcatgtgtctatttcttttatttttttc
ttcctttttccaccaaaaaccgtctacactgttattgtaaattagctgtctgtttcgtgc
ccttccccatctctcacccaagttttttgtgttttcacgcgccctataatttgtctttgt
tattatatctccctatacttgatgactatacgcttagttgtttataggtgatcattactc
tgaaagttcgatcttttttatttgtaattttcagcagcagtagaagctgggcgagatcgg
gcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAGCCTGAACAGATCTCTTTCCCG 557 185 938 Antisense
TTTCCCGTCATTTTTCATGTGTCTA 18 671 956 Antisense
CATGTGTCTATTTCTTTTATTTTTT 619 209 971 Antisense
TTCCACCAAAAACCGTCTACACTGT 338 691 1005 Antisense
TAAATTAGCTGTCTGTTTCGTGCCC 554 641 1035 Antisense
CCATCTCTCACCCAAGTTTTTTGTG 334 271 1064 Antisense
TTTTCACGCGCCCTATAATTTGTCT 292 675 1089 Antisense
TTGTCTTTGTTATTATATCTCCCTA 140 709 1108 Antisense
ATATCTCCCTATACTTGATGACTAT 472 19 1122 Antisense
GGTGATCATTACTCTGAAAGTTCGA 401 499 1164 Antisense
AGTAGAAGCTGGGCGAGATCGGGCG 289 63 1216 Antisense
Sequence Source Affymetrix Proprietary Database