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[173896_s_at] C. familiaris signal sequence receptor beta

Description CEC5002 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T04G9.5 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C09500 /WB_GENE_ID=T04G9.5 /WP=CE04886 /CHR=X /FEA=Genomic Cluster /DEF=C. familiaris signal sequence receptor beta; C.elegans cDNA clone yk172b3 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 01      6grp_high1_10_10 > 10      4grp_highest_8_8 > 10      4grp_high_8_8 > 54      6grp_highest_nonorm > 15      6grp_total > 13      4grp_total > 57      6grp_total_sub > Decrease      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6307
1 2 3 4 range
A 4869.9
(-2.7)
P 		9894
(2.8)
P 		10064.4
(3)
P 		4591.6
(-3)
P 		5473
B 5103.8
(-2.7)
P 		8819.3
(2.4)
P 		9255.1
(3)
P 		4877.5
(-3)
P 		4378
C 5723.4
(-0.6)
P 		8215.6
(2.5)
P 		8636.9
(3)
P 		3757.9
(-3)
P 		4879
avr 5232.4
(-2) 		8976.3
(2.6) 		9318.8
(3) 		4409
(-3) 		4910

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5125
1 2 3 4 5 6 range
A 7498.4
(3)
P 		4560.4
(-0.8)
P 		5433.3
(0.3)
P 		5041.5
(-0.2)
P 		4952.6
(-0.3)
P 		2826
(-3)
P 		4672
B 7176.8
(3)
P 		5922.8
(1.2)
P 		6591.6
(2.2)
P 		6088.2
(1.5)
P 		4808.7
(-0.3)
P 		2913.6
(-3)
P 		4263
C 6077.5
(1.8)
P 		6209
(1.9)
P 		4918.8
(0.3)
P 		7030.2
(3)
P 		4640.3
(-0.1)
P 		2373.9
(-3)
P 		4656
avr 6917.6
(3) 		5564.1
(1.1) 		5647.9
(1.2) 		6053.3
(1.8) 		4800.5
(-0) 		2704.5
(-3) 		4213
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2377
1 2 3 4 range
A 1773.1
(0.4)
P 		2147.7
(1.5)
P 		2631
(3)
P 		672.1
(-3)
P 		1959
B 1627.6
(0.1)
P 		2178.2
(3)
P 		2144.6
(2.8)
P 		1039.4
(-3)
P 		1139
C 1894.6
(0.2)
P 		2362
(1.4)
P 		3010.2
(3)
P 		633.6
(-3)
P 		2377
avr 1765.1
(0.3) 		2229.3
(1.8) 		2595.3
(3) 		781.7
(-3) 		1814

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1809
1 2 3 4 5 6 range
A 1382.3
(1.5)
P 		1621.9
(3)
P 		1183.3
(0.2)
P 		1278.6
(0.8)
P 		1494.5
(2.2)
P 		688
(-3)
P 		934
B 2497.2
(3)
P 		1971.4
(0.8)
P 		1600.6
(-0.8)
P 		1612.5
(-0.8)
P 		1953.7
(0.7)
P 		1086.5
(-3)
P 		1411
C 2252.6
(3)
P 		1894.5
(1.5)
P 		1251.9
(-1.1)
P 		1413.8
(-0.5)
P 		1501.5
(-0.1)
P 		794.7
(-3)
P 		1458
avr 2044
(3) 		1829.3
(1.9) 		1345.3
(-0.5) 		1435
(-0.1) 		1649.9
(1) 		856.4
(-3) 		1188
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173896_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26223
Sequence Type Exemplar sequence
Representative Public ID CEC5002 NCBI
Target Description CEC5002 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=T04G9.5 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C09500 /WB_GENE_ID=T04G9.5 /WP=CE04886 /CHR=X /FEA=Genomic Cluster /DEF=C. familiaris signal sequence receptor beta; C.elegans cDNA clone yk172b3 : 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_075749(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075749 NCBI Caenorhabditis elegans T04G9.5 (T04G9.5) mRNA, complete cds. 11/11 None
SNAP00000034730 ENSEMBL cdna:SNAP chromosome:CEL140:X:767270:768064:-1 11/11 None
GENEFINDER00000034743 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:767270:768064:-1 11/11 None
T04G9.5.1 ENSEMBL cdna:known chromosome:CEL140:X:767042:768068:-1 gene:T04G9.5 11/11 None
T04G9.5.2 ENSEMBL cdna:known chromosome:CEL140:X:767055:768069:-1 gene:T04G9.5 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
chrX:767065-768065(-) 100.0 100.0
Public Domain and Genome References
Gene Title C. familiaris signal sequence receptor beta
Ensembl T04G9.5
Entrez Gene 180422 Entrez gene
SwissProt Q22169 EMBL-EBI
WormBase CE04886 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1589932_S_AT signal sequence receptor, beta (translocon-associated protein beta) cfa
CANINE_2:CFA.2734.1.S1_S_AT signal sequence receptor, beta (translocon-associated protein beta) cfa
CANINE:1592615_AT Signal sequence receptor beta subunit cfa
DROSOPHILA_2:1634773_AT Signal sequence receptor dm
DROSGENOME1:153699_AT Signal sequence receptor dm
CHICKEN:GGA.7437.1.S1_S_AT signal sequence receptor, beta (translocon-associated protein beta) gga
HG-U133_PLUS_2:200652_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HG-FOCUS:200652_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HG-U133A_2:200652_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HG-U133A:200652_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HU35KSUBA:HUM_ALU_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HU35KSUBB:HUM_ALU_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HU35KSUBC:HUM_ALU_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HU35KSUBD:HUM_ALU_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HUGENEFL:HUM_ALU_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HC-G110:HUM_ALU_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HUGENEFL:X74104_AT signal sequence receptor, beta (translocon-associated protein beta) hs
U133_X3P:G6552341_3P_AT signal sequence receptor, beta (translocon-associated protein beta) hs
HG-U95AV2:36147_AT signal sequence receptor, beta (translocon-associated protein beta) hs
MU11KSUBA:AA683950_AT signal sequence receptor, beta mm
MU11KSUBB:MSA.7335.0_F_AT signal sequence receptor, beta mm
MU11KSUBB:MSA.10008.0_F_AT signal sequence receptor, beta mm
MG-U74AV2:101061_AT signal sequence receptor, beta mm
MOE430A:1449930_A_AT signal sequence receptor, beta mm
MOUSE430A_2:1449930_A_AT signal sequence receptor, beta mm
MOUSE430_2:1449930_A_AT signal sequence receptor, beta mm
MU19KSUBB:TC34411_AT Signal sequence receptor, beta, mRNA (cDNA clone MGC:6370 IMAGE:3497894) mm
RG-U34C:RC_AI103793_AT signal sequence receptor, beta (predicted) rn
RAE230A:1373185_AT signal sequence receptor, beta (predicted) rn
RAT230_2:1373185_AT signal sequence receptor, beta (predicted) rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5783 endoplasmic reticulum inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_508150 T04G9.5 [Caenorhabditis elegans] gb|AAA82458.1| Hypothetical protein T04G9.5 [Caenorhabditis elegans] 1.0E-105
blast CAE63626 Hypothetical protein CBG08120 [Caenorhabditis briggsae] 3.0E-95
Protein Domains
Database ID Description E-Value
Pfam IPR008856 EMBL-EBI Translocon-associated beta 1.1E-107
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508150.1 1 151-173
T04G9.5.1 1 151-173
T04G9.5.2 1 151-173
SNAP00000034730 1 151-173
GENEFINDER00000034743 1 151-173
Sequence
Target Sequence 
>C. ELEGANS:173896_S_AT
ccagcgcagaaggtcaccatcgacgatcgtcactcgttcccaaccaactcgttcgacatc
gtcaagggacttctcttcgtgcacttcgagcagatcccagccggaagcaacgtgacccac
tcagttgtcatccgcccaagagccttcggattcttcaactacaccgccgcccaggtcact
tactacaccgacaacgagaaccatcacgtcacccttaccaacactcctggagaaggatac
atctaccgccaacgcgagtacgacagacgatttgctccaaagtacacctacttcctcgtc
ttcttcctcatcgtcgccccaaccactctcggatccttccttctcttccaacaatcaaag
gctcgcttcccaaatgttatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAGCGCAGAAGGTCACCATCGACG 550 273 182 Antisense
CACCATCGACGATCGTCACTCGTTC 240 201 196 Antisense
GACATCGTCAAGGGACTTCTCTTCG 452 369 236 Antisense
TTCTCTTCGTGCACTTCGAGCAGAT 20 691 252 Antisense
CAGATCCCAGCCGGAAGCAACGTGA 656 205 272 Antisense
CAACGTGACCCACTCAGTTGTCATC 675 187 289 Antisense
AAGAGCCTTCGGATTCTTCAACTAC 185 155 319 Antisense
CAGGTCACTTACTACACCGACAACG 491 187 353 Antisense
CATCTACCGCCAACGCGAGTACGAC 22 211 421 Antisense
GTACGACAGACGATTTGCTCCAAAG 267 459 439 Antisense
AAAGGCTCGCTTCCCAAATGTTATC 77 111 538 Antisense
Sequence Source Affymetrix Proprietary Database