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[173390_s_at]

Description AU116398_rc /REP_DB=TREMBL Accession /GB=AU116398 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk744c12 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 20      4grp_highest_8_8 > 49      4grp_high_8_8 > 41      6grp_highest_nonorm > 32      6grp_total > 40      4grp_total > 54      6grp_highest_sub > 02_03      6grp_cgc > 72      6grp_cgc_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 797
1 2 3 4 range
A 1219.1
(3)
P 		826.4
(-0.3)
P 		801.4
(-0.5)
P 		505
(-3)
P 		714
B 1302.1
(3)
P 		826.2
(-1)
P 		674.8
(-2.2)
P 		584.8
(-3)
P 		717
C 1226.8
(3)
P 		667.6
(-2.1)
P 		769.8
(-1.2)
P 		568.6
(-3)
P 		658
avr 1249.3
(3) 		773.4
(-1.1) 		748.7
(-1.3) 		552.8
(-3) 		697

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 740
1 2 3 4 5 6 range
A 1353.9
(1.6)
P 		1144
(-0.4)
P 		1510.1
(3)
P 		1280.2
(0.9)
P 		857.8
(-3)
P 		943.2
(-2.2)
P 		652
B 1333.2
(1.9)
P 		1415
(3)
P 		1340
(2)
P 		1261.9
(0.9)
P 		969.9
(-3)
P 		1106.4
(-1.2)
P 		445
C 834.4
(-3)
P 		1573.9
(3)
P 		1341.4
(1.1)
P 		1542.4
(2.7)
P 		833.5
(-3)
P 		964.8
(-1.9)
P 		740
avr 1173.8
(0.4) 		1377.6
(2.8) 		1397.2
(3) 		1361.5
(2.6) 		887.1
(-3) 		1004.8
(-1.6) 		510
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 370
1 2 3 4 range
A 443.9
(3)
P 		179.4
(-1.3)
P 		209.5
(-0.8)
P 		73.9
(-3)
P 		370
B 415.2
(3)
P 		204.1
(-1.4)
P 		156.4
(-2.3)
P 		124.6
(-3)
P 		291
C 406.1
(3)
P 		191.9
(-1.1)
P 		268.3
(0.3)
P 		95.9
(-3)
P 		310
avr 421.7
(3) 		191.8
(-1.3) 		211.4
(-0.9) 		98.1
(-3) 		324

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 251
1 2 3 4 5 6 range
A 249.6
(-2.3)
P 		406.9
(3)
P 		328.9
(0.4)
P 		324.7
(0.2)
P 		258.8
(-2)
P 		229.6
(-3)
P 		177
B 463.9
(2.7)
P 		471
(3)
P 		325.4
(-3)
P 		334.2
(-2.6)
P 		394.1
(-0.2)
P 		412.6
(0.6)
P 		146
C 309.3
(-1.9)
P 		480.3
(3)
P 		341.4
(-1)
P 		310.2
(-1.8)
P 		269.7
(-3)
P 		323
(-1.5)
P 		211
avr 340.9
(-1.6) 		452.7
(3) 		331.9
(-2) 		323
(-2.4) 		307.5
(-3) 		321.7
(-2.4) 		145
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173390_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.28017
Sequence Type Exemplar sequence
Representative Public ID AU116398 NCBI
Target Description AU116398_rc /REP_DB=TREMBL Accession /GB=AU116398 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk744c12 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript 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_065718(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065718 NCBI Caenorhabditis elegans Gro-1 OPeron gene family member (gop-3) (gop-3) mRNA, complete cds. 11/11 A 
C34E10.1.2 ENSEMBL cdna:known chromosome:CEL140:III:5260649:5263794:1 gene:C34E10.1 11/11 A 
C34E10.1.3 ENSEMBL cdna:known chromosome:CEL140:III:5260650:5263794:1 gene:C34E10.1 11/11 None
C34E10.1.1 ENSEMBL cdna:known chromosome:CEL140:III:5260651:5263794:1 gene:C34E10.1 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:5262548-5263730(+) 98.04 98.04
Public Domain and Genome References
Gene Title
Gene Symbol gop-3
Ensembl C34E10.1
Entrez Gene 175723 Entrez gene
WormBase CE26880 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1594727_AT similar to SAM50-like protein CGI-51 cfa
CANINE:1583394_S_AT similar to SAM50-like protein CGI-51 cfa
CANINE_2:CFA.11724.1.A1_S_AT similar to SAM50-like protein CGI-51 cfa
CANINE_2:CFA.20945.1.S1_S_AT similar to SAM50-like protein CGI-51 cfa
CANINE_2:CFA.6368.1.A1_S_AT similar to SAM50-like protein CGI-51 cfa
DROSOPHILA_2:1630893_AT dm
DROSGENOME1:142447_AT dm
CHICKEN:GGA.10268.1.S1_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) gga
HG-U133_PLUS_2:201570_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133A:201570_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133A_2:201570_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HU35KSUBB:RC_H74276_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133A:201569_S_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:201569_S_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133A_2:201569_S_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
U133_X3P:G7661541_3P_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
U133_X3P:G7661541_3P_A_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U95AV2:34845_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
U133_X3P:HS.4877.1.S1_3P_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
U133_X3P:HS.132895.0.A1_3P_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:230396_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133B:230396_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133_PLUS_2:243239_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U133B:243239_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U95C:57320_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HG-U95D:78302_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
HU35KSUBD:RC_AA424675_AT Sorting and assembly machinery component 50 homolog (S. cerevisiae) hs
MOE430A:1428068_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) mm
MOUSE430A_2:1428068_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) mm
MOUSE430_2:1428068_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) mm
MOUSE430A_2:1455800_X_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) mm
MOE430A:1455800_X_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) mm
MOUSE430_2:1455800_X_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) mm
MU11KSUBA:AA050066_S_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) mm
MG-U74AV2:95690_AT sorting and assembly machinery component 50 homolog (S. cerevisiae) mm
RG-U34C:RC_AI232741_AT similar to Protein CGI-51 rn
RAE230A:1388380_AT similar to Protein CGI-51 rn
RAT230_2:1388380_AT similar to Protein CGI-51 rn
YEAST_2:1774480_AT Essential component of the Sorting and Assembly Machinery (SAM or Tob complex) of the mitochondrial outer membrane, which binds precursors of beta-barrel proteins and facilitates their outer membrane insertion; homologous to bacterial Omp85 Sc
Protein Similarities
Method ID Description E-Value
blast AAA19063 Gro-1 operon gene protein 3 [Caenorhabditis elegans] ref|NP_498119.1| Gro-1 OPeron gene family member (gop-3) [Caenorhabditis elegans] gb|AAL14110.1| GOP-3 [Caenorhabditis elegans] sp|P46576|SAM50_CAEEL SAM50-like protein gop-3 (Gro-1 operon protein 3) 0.0
blast CAE73672 Hypothetical protein CBG21181 [Caenorhabditis briggsae] 1.0E-164
blast AAH60470 MGC68698 protein [Xenopus laevis] 1.0E-54
Protein Domains
Database ID Description E-Value
Pfam IPR000184 EMBL-EBI Bacterial surface antigen (D15) 1.1E-24
Sequence
Target Sequence 
>C. ELEGANS:173390_S_AT
atcagccggatttggactcgcattcgtgttcaaaagtattttccggctggaactcaacta
cacgtatccattgaaatatgtgctcggcgattcattgctcggtggattccatattggagc
tggtgtcaacttcttgtagagattaattggatgcaangcacccctcnnnnngatgnnnnn
gnnnnncgataaattcacagaatttcagttcnnnnnctnnnnnntttattgttattttca
tcgtaatgctgtg

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
ATCAGCCGGATTTGGACTCGCATTC 201 29 36 Antisense
GGATTTGGACTCGCATTCGTGTTCA 630 509 43 Antisense
GGACTCGCATTCGTGTTCAAAAGTA 367 525 49 Antisense
GTATTTTCCGGCTGGAACTCAACTA 299 445 71 Antisense
GGAACTCAACTACACGTATCCATTG 578 529 84 Antisense
CGTATCCATTGAAATATGTGCTCGG 493 247 98 Antisense
ATATGTGCTCGGCGATTCATTGCTC 534 19 111 Antisense
CATTGCTCGGTGGATTCCATATTGG 127 217 128 Antisense
GGTGGATTCCATATTGGAGCTGGTG 616 499 136 Antisense
GGAGCTGGTGTCAACTTCTTGTAGA 22 523 151 Antisense
TTGTTATTTTCATCGTAATGCTGTG 553 703 264 Antisense
Sequence Source Affymetrix Proprietary Database