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[192859_at] tetracycline resistance protein like

Description C39E9.10 /REP_DB=WormBase Gene ID /WP=CE05393 /TR=Q18545 /GB=CAA94337.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=tetracycline resistance protein like
Cluster 6grp_highest_10_10 > 70      6grp_high1_10_10 > 05      4grp_high_8_8 > 51      6grp_highest_nonorm > 70      6grp_total > 05      4grp_total > 60      6grp_highest_sub > De      6grp_high1_sub > De      6grp_rule_based > S1      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 207
1 2 3 4 range
A 285.6
(1.6)
P 		321.2
(2.7)
P 		333.1
(3)
P 		125.9
(-3)
P 		207
B 267.4
(3)
P 		260.7
(2.7)
P 		249.6
(2.2)
P 		132
(-3)
P 		135
C 284.8
(3)
P 		277.2
(2.7)
P 		276.5
(2.7)
P 		134.8
(-3)
A 		150
avr 279.3
(2.7) 		286.4
(3) 		286.4
(3) 		130.9
(-3) 		156

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 309
1 2 3 4 5 6 range
A 455.3
(3)
P 		267.4
(-1)
P 		209.1
(-2.3)
P 		233.6
(-1.8)
P 		230.9
(-1.8)
P 		176.6
(-3)
P 		279
B 349.9
(3)
P 		260.7
(-0.4)
P 		197.1
(-2.9)
P 		226.5
(-1.7)
P 		291.5
(0.8)
P 		193.7
(-3)
P 		156
C 315.2
(3)
P 		311.8
(2.9)
P 		241.3
(0.4)
P 		204.5
(-0.9)
P 		155.8
(-2.7)
P 		146.3
(-3)
P 		169
avr 373.5
(3) 		280
(0.2) 		215.8
(-1.7) 		221.5
(-1.5) 		226.1
(-1.4) 		172.2
(-3) 		201
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 86
1 2 3 4 range
A 104
(3)
P 		69.7
(0.6)
P 		87.1
(1.8)
P 		18.4
(-3)
P 		86
B 85.3
(3)
P 		64.4
(0.8)
P 		57.8
(0.1)
P 		28.1
(-3)
P 		57
C 94.3
(2.8)
P 		79.7
(1.6)
P 		96.4
(3)
P 		22.7
(-3)
A 		74
avr 94.5
(3) 		71.3
(1.1) 		80.4
(1.8) 		23.1
(-3) 		71

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 81
1 2 3 4 5 6 range
A 83.9
(1.7)
P 		95.1
(3)
P 		45.5
(-2.7)
P 		59.3
(-1.1)
P 		69.7
(0.1)
P 		43
(-3)
P 		52
B 121.7
(3)
P 		86.8
(0.2)
P 		47.9
(-3)
P 		60
(-2)
P 		118.4
(2.7)
P 		72.2
(-1)
P 		74
C 116.8
(3)
P 		95.1
(1.3)
P 		61.4
(-1.4)
P 		41.1
(-3)
P 		50.4
(-2.3)
P 		49
(-2.4)
P 		76
avr 107.5
(3) 		92.3
(1.4) 		51.6
(-3) 		53.5
(-2.8) 		79.5
(-0) 		54.7
(-2.7) 		56
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192859_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8967
Sequence Type Exemplar sequence
Representative Public ID C39E9.10 NCBI
Target Description C39E9.10 /REP_DB=WormBase Gene ID /WP=CE05393 /TR=Q18545 /GB=CAA94337.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=tetracycline resistance protein like
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_070112(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070112 NCBI Caenorhabditis elegans C39E9.10 (C39E9.10) mRNA, complete cds. 11/11 None
SNAP00000026308 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13086977:13089454:1 11/11 None
GENEFINDER00000026325 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13086977:13089454:1 11/11 None
C39E9.10 ENSEMBL cdna:known chromosome:CEL140:IV:13086975:13089578:1 gene:C39E9.10 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:13086982-13089460(+) 100.0 100.0
Public Domain and Genome References
Gene Title tetracycline resistance protein like
Ensembl C39E9.10
Entrez Gene 178256 Entrez gene
SwissProt Q18545 EMBL-EBI
WormBase CE05393 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:14332_AT transporter-related at
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
6955 immune response inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5164 tumor necrosis factor receptor binding inferred from electronic annotation QuickGO AmiGO
5215 transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA94337 Hypothetical protein C39E9.10 [Caenorhabditis elegans] ref|NP_502513.1| C39E9.10 [Caenorhabditis elegans] 0.0
blast CAE58662 Hypothetical protein CBG01831 [Caenorhabditis briggsae] 0.0
blast CAE61389 Hypothetical protein CBG05238 [Caenorhabditis briggsae] 1.0E-132
Protein Domains
Database ID Description E-Value
Pfam IPR005828 EMBL-EBI General substrate transporter 2.1E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502513.1 11 46-68,75-94,99-121,134-156,166-188,217-239,276-298,319-338,343-365,385-407,422-444
C39E9.10 11 46-68,75-94,99-121,134-156,166-188,217-239,276-298,319-338,343-365,385-407,422-444
SNAP00000026308 11 46-68,75-94,99-121,134-156,166-188,217-239,276-298,319-338,343-365,385-407,422-444
GENEFINDER00000026325 11 46-68,75-94,99-121,134-156,166-188,217-239,276-298,319-338,343-365,385-407,422-444
Sequence
Target Sequence 
>C. ELEGANS:192859_AT
ggagcaatcaccacagctggaggactcatcggtgtcattttcggatcgatgctctccaaa
tggctggtagctggatggggaccattcagaagactccagacagacagagcacagcctttg
gtggctggtggcggggcgttgcttgctgctccatttttacttattggaatgatctttgga
gataagagcttggtgttgctgtacattatgatcttctttggaatcaccttcatgtgcttc
aactggggtctgaacatcgatatgttgacgactgtcatccacccgaatcggcgaagtact
gctttctcctacttcgtactggtatcccatttgtttggcgacgcttctggtccgtatctc
atcgggttaatctccgacgcaatccgccacggatccacatatcctaaagatcaatatcat
tcattggtaagtgccacgtattgctgcgtggcactgcttttgctctctgccggactgtac
tttgtgtcctcactcacgctggtctcggatcggaagaagttccgagcggaaatgggtctc
gatgatcttcaatccaagcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGCAATCACCACAGCTGGAGGAC 658 519 850 Antisense
GACTCATCGGTGTCATTTTCGGATC 60 375 872 Antisense
GATGCTCTCCAAATGGCTGGTAGCT 1 415 897 Antisense
TTGGAATCACCTTCATGTGCTTCAA 452 709 1067 Antisense
CGAATCGGCGAAGTACTGCTTTCTC 392 251 1133 Antisense
CCTACTTCGTACTGGTATCCCATTT 659 265 1157 Antisense
TATCCCATTTGTTTGGCGACGCTTC 204 659 1172 Antisense
TTCTGGTCCGTATCTCATCGGGTTA 247 693 1194 Antisense
CACGTATTGCTGCGTGGCACTGCTT 621 195 1284 Antisense
TCTCTGCCGGACTGTACTTTGTGTC 184 609 1313 Antisense
GTCTCGATGATCTTCAATCCAAGCC 397 471 1385 Antisense
Sequence Source Affymetrix Proprietary Database