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[189506_at] transport protein

Description C53B4.1 /REP_DB=WormBase Gene ID /WP=CE03087 /TR=Q18795 /GB=CAA92450.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=transport protein
Cluster 6grp_high1_10_10 > 11      4grp_high_8_8 > 19      6grp_total > 23      4grp_total > 29      6grp_high1_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 73
1 2 3 4 range
A 88.3
(0.2)
P 		69.8
(-1.3)
P 		49.2
(-3)
A 		121.7
(3)
P 		73
B 106.2
(3)
P 		80.6
(-0.4)
P 		60.9
(-3)
A 		64.7
(-2.5)
P 		45
C 107.2
(1.7)
P 		101.1
(1.1)
P 		61.9
(-3)
P 		119.3
(3)
P 		57
avr 100.6
(2.8) 		83.8
(0.6) 		57.3
(-3) 		101.9
(3) 		45

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 65
1 2 3 4 5 6 range
A 98.2
(3)
P 		87
(1.4)
P 		88.1
(1.6)
P 		95.5
(2.6)
P 		62.7
(-2)
P 		55.8
(-3)
A 		42
B 104.8
(1.3)
P 		89.1
(-0.4)
P 		120.4
(3)
P 		99
(0.6)
P 		91.6
(-0.2)
P 		65.8
(-3)
P 		55
C 100.1
(1.6)
P 		113.1
(3)
P 		91.1
(0.7)
P 		80.4
(-0.5)
P 		56.7
(-3)
P 		65.1
(-2.1)
P 		56
avr 101
(3) 		96.4
(2.3) 		99.9
(2.8) 		91.6
(1.5) 		70.3
(-1.7) 		62.2
(-3) 		39
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 23
1 2 3 4 range
A 32.2
(3)
P 		15.1
(-2.3)
P 		12.9
(-3)
A 		17.8
(-1.5)
P 		19
B 33.9
(3)
P 		19.9
(-1.2)
P 		14.1
(-2.9)
A 		13.8
(-3)
P 		20
C 35.5
(3)
P 		29.1
(0.5)
P 		21.6
(-2.4)
P 		20.1
(-3)
P 		15
avr 33.9
(3) 		21.4
(-1.2) 		16.2
(-3) 		17.2
(-2.7) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 24
1 2 3 4 5 6 range
A 18.1
(-1.4)
P 		30.9
(3)
P 		19.2
(-1.1)
P 		24.2
(0.7)
P 		18.9
(-1.2)
P 		13.6
(-3)
A 		17
B 36.5
(2.7)
P 		29.7
(-0.5)
P 		29.2
(-0.8)
P 		26.2
(-2.2)
P 		37.2
(3)
P 		24.5
(-3)
P 		13
C 37.1
(3)
P 		34.5
(2.3)
P 		23.2
(-1)
P 		16.2
(-3)
P 		18.4
(-2.4)
P 		21.8
(-1.4)
P 		21
avr 30.6
(2.4) 		31.7
(3) 		23.9
(-1) 		22.2
(-1.9) 		24.8
(-0.5) 		20
(-3) 		12
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189506_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9580
Sequence Type Exemplar sequence
Representative Public ID C53B4.1 NCBI
Target Description C53B4.1 /REP_DB=WormBase Gene ID /WP=CE03087 /TR=Q18795 /GB=CAA92450.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=transport protein
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_069155(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069155 NCBI Caenorhabditis elegans C53B4.1 (C53B4.1) mRNA, complete cds. 11/11 None
SNAP00000003705 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8968451:8970545:1 10/11 None
GENEFINDER00000003713 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8966192:8970569:1 10/11 None
C53B4.1 ENSEMBL cdna:known chromosome:CEL140:IV:8968156:8970545:1 gene:C53B4.1 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
chrIV:8968161-8970551(+) 98.33 100.0
Public Domain and Genome References
Gene Title transport protein
Ensembl C53B4.1
Entrez Gene 183742 Entrez gene
SwissProt Q18795 EMBL-EBI
WormBase CE03087 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6306 DNA methylation inferred from electronic annotation QuickGO AmiGO
6810 transport 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
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
5215 transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA92450 Hypothetical protein C53B4.1 [Caenorhabditis elegans] ref|NP_501556.1| C53B4.1 [Caenorhabditis elegans] 0.0
blast CAE74077 Hypothetical protein CBG21731 [Caenorhabditis briggsae] 0.0
blast CAE74077 Hypothetical protein CBG21731 [Caenorhabditis briggsae] 1.0E-178
blast CAE74077 Hypothetical protein CBG21731 [Caenorhabditis briggsae] 1.0E-156
blast CAA92451 Hypothetical protein C53B4.2 [Caenorhabditis elegans] ref|NP_501555.2| C53B4.2 [Caenorhabditis elegans] 1.0E-151
blast CAB16524 Hypothetical protein Y57G11C.23 [Caenorhabditis elegans] ref|NP_502801.1| Y57G11C.23 [Caenorhabditis elegans] 1.0E-146
Protein Domains
Database ID Description E-Value
Pfam IPR005828 EMBL-EBI General substrate transporter 1.0E-7
Pfam IPR005828 EMBL-EBI General substrate transporter 1.0E-7
Pfam IPR005828 EMBL-EBI General substrate transporter 1.0E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501556.1 10 24-46,115-137,144-166,170-192,231-253,304-321,333-352,367-389,396-418,458-477
C53B4.1 10 24-46,115-137,144-166,170-192,231-253,304-321,333-352,367-389,396-418,458-477
SNAP00000003705 7 82-104,111-133,137-159,198-220,271-288,300-319,334-356
GENEFINDER00000003713 7 467-489,591-610,615-637,677-699,750-767,779-798,813-835
Sequence
Target Sequence 
>C. ELEGANS:189506_AT
tgtccggtttagtactctcaatcgctcaatttataattggtatgacagagccatatttaa
caggattaggccgccgagttctctttcttatcgctcaatttattgctatgctgtgttaca
tttgtattttgatatgtctttatttaaattggaagggctcattcttatatctttctgcct
atacattagcttatgctactcaatctctttgtctggaagctgcatatctttctcttgtgg
aacttatgccaactgatgttagagccactgcaggatcaactgccaacatttgtatgaaaa
ttggaactattttggcaaccttaacgaagccgttgaagtttgcatatgaaccatcactat
tcttcattaatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTCCGGTTTAGTACTCTCAATCGC 597 557 1028 Antisense
AACAGGATTAGGCCGCCGAGTTCTC 531 133 1086 Antisense
TTCTCTTTCTTATCGCTCAATTTAT 571 691 1106 Antisense
AGGGCTCATTCTTATATCTTTCTGC 242 59 1181 Antisense
ATCTTTCTGCCTATACATTAGCTTA 599 31 1196 Antisense
GCTTATGCTACTCAATCTCTTTGTC 199 305 1216 Antisense
AATCTCTTTGTCTGGAAGCTGCATA 288 169 1229 Antisense
GCTGCATATCTTTCTCTTGTGGAAC 476 297 1246 Antisense
TGCCAACTGATGTTAGAGCCACTGC 134 583 1274 Antisense
GAGCCACTGCAGGATCAACTGCCAA 448 385 1289 Antisense
GAACCATCACTATTCTTCATTAATT 17 347 1375 Antisense
Sequence Source Affymetrix Proprietary Database