[Home] | [Total List]

[173000_s_at]

Description C34559_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=C34559 /DEF=C.elegans cDNA clone yk404a8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 77      4grp_highest_8_8 > 30      4grp_high_8_8 > 05      6grp_highest_nonorm > 84      6grp_total > 77      4grp_total > 04      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2752
1 2 3 4 range
A 1032.1
(-1.6)
P 		549.8
(-2.9)
P 		499.9
(-3)
P 		2703
(3)
P 		2203
B 950.1
(-1.9)
P 		446.8
(-3)
P 		437.9
(-3)
P 		3190.1
(3)
P 		2752
C 774.8
(-2.2)
P 		458.5
(-3)
P 		473.1
(-3)
P 		2926.7
(3)
P 		2468
avr 919
(-1.9) 		485
(-3) 		470.3
(-3) 		2939.9
(3) 		2470

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 384
1 2 3 4 5 6 range
A 456.3
(-3)
P 		642
(0.4)
P 		538.3
(-1.5)
P 		584.4
(-0.7)
P 		583.4
(-0.7)
P 		785.6
(3)
P 		329
B 630.1
(-1)
P 		564.4
(-2.2)
P 		524.5
(-3)
P 		540.8
(-2.7)
P 		651
(-0.6)
P 		840.4
(3)
P 		316
C 575.3
(-1.8)
P 		573
(-1.9)
P 		518.4
(-3)
P 		556.5
(-2.2)
P 		527
(-2.8)
P 		803.8
(3)
P 		285
avr 553.9
(-2.4) 		593.1
(-1.6) 		527.1
(-3) 		560.6
(-2.3) 		587.1
(-1.7) 		809.9
(3) 		283
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 578
1 2 3 4 range
A 375.8
(2.6)
P 		119.3
(-3)
P 		130.7
(-2.8)
P 		395.7
(3)
P 		276
B 303
(-0.9)
P 		110.4
(-2.9)
P 		101.5
(-3)
P 		679.8
(3)
P 		578
C 256.5
(-0.9)
P 		131.8
(-3)
P 		164.9
(-2.5)
P 		493.5
(3)
P 		362
avr 311.8
(-0.1) 		120.5
(-3) 		132.4
(-2.8) 		523
(3) 		403

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 229
1 2 3 4 5 6 range
A 84.1
(-3)
P 		228.3
(3)
P 		117.2
(-1.6)
P 		148.2
(-0.3)
P 		176
(0.8)
P 		191.3
(1.5)
P 		144
B 219.2
(-0)
P 		187.9
(-1)
P 		127.4
(-3)
P 		143.2
(-2.5)
P 		264.5
(1.4)
P 		313.4
(3)
P 		186
C 213.2
(0.9)
P 		174.9
(-0.6)
P 		132
(-2.2)
P 		111.9
(-3)
P 		170.5
(-0.8)
P 		269.1
(3)
P 		157
avr 172.2
(-0.9) 		197
(0.2) 		125.5
(-3) 		134.4
(-2.6) 		203.7
(0.5) 		257.9
(3) 		132
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173000_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26342
Sequence Type Exemplar sequence
Representative Public ID C34559 NCBI
Target Description C34559_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=C34559 /DEF=C.elegans cDNA clone yk404a8 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_070140(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070140 NCBI Caenorhabditis elegans JC8.2 (JC8.2) mRNA, complete cds. 11/11 A 
SNAP00000008998 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13233105:13239381:-1 11/11 None
GENEFINDER00000009014 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13233105:13236576:-1 11/11 None
JC8.2.2 ENSEMBL cdna:known chromosome:CEL140:IV:13232912:13236554:-1 gene:JC8.2 11/11 None
JC8.2.1 ENSEMBL cdna:known chromosome:CEL140:IV:13232912:13236556:-1 gene:JC8.2 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
chrIV:13233064-13234375(-) 99.0 99.0
Public Domain and Genome References
Gene Title
Ensembl JC8.2
Entrez Gene 178277 Entrez gene
SwissProt Q9NAQ2 EMBL-EBI
WormBase CE37529 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:17958_AT transducin family protein / WD-40 repeat family protein at
ATH1-121501:254593_S_AT transducin family protein / WD-40 repeat family protein at
CANINE:1588486_AT similar to Periodic tryptophan protein 1 homolog (Keratinocyte protein IEF SSP 9502) cfa
CANINE_2:CFA.10480.1.A1_AT similar to Periodic tryptophan protein 1 homolog (Keratinocyte protein IEF SSP 9502) cfa
CANINE_2:CFAAFFX.3557.1.S1_S_AT similar to Periodic tryptophan protein 1 homolog (Keratinocyte protein IEF SSP 9502) cfa
DROSOPHILA_2:1625030_AT dm
DROSGENOME1:154076_AT dm
CHICKEN:GGAAFFX.13042.1.S1_S_AT PWP1 homolog (S. cerevisiae) gga
CHICKEN:GGAAFFX.8012.1.S1_AT PWP1 homolog (S. cerevisiae) gga
HG-FOCUS:201606_S_AT PWP1 homolog (S. cerevisiae) hs
HG-U133A:201606_S_AT PWP1 homolog (S. cerevisiae) hs
HG-U133A_2:201606_S_AT PWP1 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:201606_S_AT PWP1 homolog (S. cerevisiae) hs
HG-U133A:201608_S_AT PWP1 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:201608_S_AT PWP1 homolog (S. cerevisiae) hs
HG-U133A_2:201608_S_AT PWP1 homolog (S. cerevisiae) hs
HU35KSUBC:RC_N92948_S_AT PWP1 homolog (S. cerevisiae) hs
HUGENEFL:L07758_AT PWP1 homolog (S. cerevisiae) hs
U133_X3P:G5902033_3P_A_AT PWP1 homolog (S. cerevisiae) hs
U133_X3P:HS.172589.0.S1_3P_A_AT PWP1 homolog (S. cerevisiae) hs
HG-U95AV2:40816_AT PWP1 homolog (S. cerevisiae) hs
HG-U133A:201607_AT PWP1 homolog (S. cerevisiae) hs
HG-U133A_2:201607_AT PWP1 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:201607_AT PWP1 homolog (S. cerevisiae) hs
U133_X3P:HS.172589.0.S3_3P_AT PWP1 homolog (S. cerevisiae) hs
MG-U74AV2:103413_AT PWP1 homolog (S. cerevisiae) mm
MOUSE430_2:1454142_A_AT PWP1 homolog (S. cerevisiae) mm
MOE430A:1454142_A_AT PWP1 homolog (S. cerevisiae) mm
MOUSE430A_2:1454142_A_AT PWP1 homolog (S. cerevisiae) mm
MOE430A:1417873_AT PWP1 homolog (S. cerevisiae) mm
MOUSE430A_2:1417873_AT PWP1 homolog (S. cerevisiae) mm
MOUSE430_2:1417873_AT PWP1 homolog (S. cerevisiae) mm
MU19KSUBA:TC24047_AT PWP1 homolog (S. cerevisiae) (Pwp1), mRNA mm
MU19KSUBC:TC40550_AT PWP1 homolog (S. cerevisiae) (Pwp1), mRNA mm
RG-U34B:RC_AA899371_AT similar to periodic tryptophan protein 1 homolog; periodic tryptophan protein 1 homolog (S. cerevisiae) (predicted) rn
RAE230B:1380443_AT similar to periodic tryptophan protein 1 homolog; periodic tryptophan protein 1 homolog (S. cerevisiae) (predicted) rn
RAT230_2:1380443_AT similar to periodic tryptophan protein 1 homolog; periodic tryptophan protein 1 homolog (S. cerevisiae) (predicted) rn
YEAST_2:1774541_AT Protein with WD-40 repeats involved in rRNA processing; associates with trans-acting ribosome biogenesis factors; similar to beta-transducin superfamily Sc
Protein Similarities
Method ID Description E-Value
blast CAB05230 Hypothetical protein JC8.2 [Caenorhabditis elegans] ref|NP_502541.2| JC8.2 [Caenorhabditis elegans] 0.0
blast CAE58640 Hypothetical protein CBG01808 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.55
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 4.9E-8
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.0091
Pfam IPR005062 EMBL-EBI SAC3/GANP family 2.8E-11
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.55
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 4.9E-8
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.0091
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.55
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 4.9E-8
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.0091
Sequence
Target Sequence 
>C. ELEGANS:173000_S_AT
ttctgcacttactaaaggattgctggttactgttggngaagatgagatgatgaatgtttg
gaaagttgaagacaccaatggaggaatcgaaaaagttcattcggagaagctgaccatcgg
agagctccattgtgctcaattcaatccagacgtggcagcagttctttctgttggtggaac
tgccgccgatttgatccgtatcatcgatttaaccaaatacgaaccggtcgtcaaagcatt
ctc

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCTGCACTTACTAAAGGATTGCTG 265 691 14 Antisense
CTAAAGGATTGCTGGTTACTGTTGG 685 223 25 Antisense
GGAAAGTTGAAGACACCAATGGAGG 260 527 73 Antisense
GTTCATTCGGAGAAGCTGACCATCG 647 443 108 Antisense
AAGCTGACCATCGGAGAGCTCCATT 196 149 120 Antisense
AATTCAATCCAGACGTGGCAGCAGT 682 175 151 Antisense
CAGACGTGGCAGCAGTTCTTTCTGT 342 205 160 Antisense
TTCTTTCTGTTGGTGGAACTGCCGC 625 689 175 Antisense
TGATCCGTATCATCGATTTAACCAA 315 565 205 Antisense
CATCGATTTAACCAAATACGAACCG 93 211 215 Antisense
ACGAACCGGTCGTCAAAGCATTCTC 215 89 232 Antisense
Sequence Source Affymetrix Proprietary Database