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[193563_at] transport system membrane protein

Description K11G12.3 /REP_DB=WormBase Gene ID /WP=CE02825 /GEN=smf-2 /TR=Q21433 /GB=AAC46568.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=transport system membrane protein
Cluster 6grp_total > 77      4grp_total > 02      6grp_cgc > 49      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 561
1 2 3 4 range
A 41.3
(-2.7)
P 		41.7
(-2.7)
A 		20.5
(-3)
A 		436
(3)
P 		416
B 49.1
(-2.8)
A 		29.9
(-3)
A 		39.9
(-2.9)
A 		564.1
(3)
P 		534
C 28.8
(-2.9)
A 		29.8
(-2.8)
A 		15.5
(-3)
A 		576.9
(3)
P 		561
avr 39.7
(-2.8) 		33.8
(-2.9) 		25.3
(-3) 		525.7
(3) 		500

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1274
1 2 3 4 5 6 range
A 64.4
(-2.8)
A 		25.2
(-3)
A 		55.9
(-2.9)
P 		34.8
(-3)
M 		295.8
(-1.7)
P 		1288.6
(3)
P 		1263
B 14.4
(-3)
A 		27.2
(-2.9)
A 		37.3
(-2.9)
A 		28.2
(-2.9)
A 		358.9
(-1.3)
P 		1251.3
(3)
P 		1237
C 17.5
(-3)
A 		39
(-2.9)
P 		33.2
(-2.9)
A 		61.1
(-2.8)
P 		356.1
(-1.3)
P 		1202.1
(3)
P 		1185
avr 32.1
(-3) 		30.5
(-3) 		42.1
(-2.9) 		41.4
(-2.9) 		336.9
(-1.5) 		1247.3
(3) 		1217
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 115
1 2 3 4 range
A 15
(-2)
P 		9.1
(-2.6)
A 		5.3
(-3)
A 		63.8
(3)
P 		59
B 15.7
(-2.6)
A 		7.4
(-3)
A 		9.2
(-2.9)
A 		120.2
(3)
P 		113
C 9.5
(-2.7)
A 		8.6
(-2.8)
A 		5.4
(-3)
A 		97.3
(3)
P 		92
avr 13.4
(-2.5) 		8.4
(-2.9) 		6.6
(-3) 		93.8
(3) 		87

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 462
1 2 3 4 5 6 range
A 11.9
(-2.9)
A 		9
(-3)
A 		12.2
(-2.9)
P 		8.8
(-3)
M 		89.2
(-1.4)
P 		313.7
(3)
P 		305
B 5
(-3)
A 		9
(-2.9)
A 		9.1
(-2.9)
A 		7.5
(-3)
A 		145.8
(-1.2)
P 		466.6
(3)
P 		462
C 6.5
(-3)
A 		11.9
(-2.9)
P 		8.5
(-3)
A 		12.3
(-2.9)
P 		115.2
(-1.4)
P 		402.4
(3)
P 		396
avr 7.8
(-3) 		10
(-3) 		9.9
(-3) 		9.5
(-3) 		116.7
(-1.3) 		394.2
(3) 		386
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193563_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16976
Sequence Type Exemplar sequence
Representative Public ID K11G12.3 NCBI
Target Description K11G12.3 /REP_DB=WormBase Gene ID /WP=CE02825 /GEN=smf-2 /TR=Q21433 /GB=AAC46568.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=transport system membrane 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_076730(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076730 NCBI Caenorhabditis elegans yeast SMF (divalent cation transporter) homolog family member (smf-2) (smf-2) mRNA, complete cds. 11/11 None
GENEFINDER00000013748 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6716311:6718623:-1 9/11 None
K11G12.3 ENSEMBL cdna:known chromosome:CEL140:X:6716311:6718417:-1 gene:K11G12.3 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:6716310-6718417(-) 100.0 100.0
Public Domain and Genome References
Gene Title transport system membrane protein
Gene Symbol smf-2
Ensembl K11G12.3
Entrez Gene 191766 Entrez gene
SwissProt Q21433 EMBL-EBI
WormBase CE02825 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:18118_AT NRAMP metal ion transporter 5, putative (NRAMP5) at
ATH1-121501:254640_AT NRAMP metal ion transporter 5, putative (NRAMP5) at
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
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
GO Molecular Function (view graph)
ID Description Evidence Links
5215 transporter activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC46568 Yeast smf (divalent cation transporter) homolog protein 2 [Caenorhabditis elegans] ref|NP_509131.1| yeast SMF (divalent cation transporter) homolog family member (smf-2) [Caenorhabditis elegans] 0.0
blast CAE65779 Hypothetical protein CBG10874 [Caenorhabditis briggsae] 0.0
blast AAC46569 Yeast smf (divalent cation transporter) homolog protein 1, isoform a [Caenorhabditis elegans] ref|NP_001024792.1| yeast SMF (divalent cation transporter) homolog family member (smf-1) [Caenorhabditis elegans] sp|Q21434|NRAML_CAEEL NRAMP-like transporter smf-1 0.0
blast AAU05559 Yeast smf (divalent cation transporter) homolog protein 1, isoform b [Caenorhabditis elegans] ref|NP_001024793.1| yeast SMF (divalent cation transporter) homolog family member (smf-1) [Caenorhabditis elegans] 1.0E-144
blast CAE65779 Hypothetical protein CBG10874 [Caenorhabditis briggsae] 1.0E-112
Protein Domains
Database ID Description E-Value
Pfam IPR001046 EMBL-EBI Natural resistance-associated macrophage protein 1.0E-126
Pfam IPR001046 EMBL-EBI Natural resistance-associated macrophage protein 1.0E-126
Pfam IPR001046 EMBL-EBI Natural resistance-associated macrophage protein 6.6E-55
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509131.1 9 25-44,57-79,89-111,128-150,174-196,216-238,253-275,369-391,401-423
K11G12.3 9 25-44,57-79,89-111,128-150,174-196,216-238,253-275,369-391,401-423
GENEFINDER00000013748 9 77-94,109-131,143-165,180-202,215-237,252-274,304-326,346-365,377-399
Sequence
Target Sequence 
>C. ELEGANS:193563_AT
aaccagagcggttgcaatcactccaacgttgatcctctgcataaaagcccacggcatcaa
aaatttgacaggtatgaatgactttctaaactgtgttcaaatggtacagctaccgtttgc
attgattccgatgattacatttacttccagtaagcggattatgcacaattttcgaacttc
caaacctctacaatacttttctattatctgtggaattattacaatcgggatcaacgtgta
cttcattttccagtatgtgactgaaaatttcggcactggttggctgatttttgttattat
tgggccatttactttgttatacattgcttttatcctttatctggctatctactgtttggt
tgcttgcgaacttatgaacgacactgtgaaccttccgggatttgattttcatagaacact
ggaactggatgctccgtggatcacag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACCAGAGCGGTTGCAATCACTCCA 131 149 933 Antisense
TGATCCTCTGCATAAAAGCCCACGG 370 565 962 Antisense
ACAGCTACCGTTTGCATTGATTCCG 369 109 1038 Antisense
GCACAATTTTCGAACTTCCAAACCT 271 317 1095 Antisense
TCCAAACCTCTACAATACTTTTCTA 703 585 1111 Antisense
GATCAACGTGTACTTCATTTTCCAG 24 423 1161 Antisense
ATTTCGGCACTGGTTGGCTGATTTT 5 17 1199 Antisense
TACATTGCTTTTATCCTTTATCTGG 222 645 1252 Antisense
GGCTATCTACTGTTTGGTTGCTTGC 112 539 1275 Antisense
TGAACGACACTGTGAACCTTCCGGG 632 573 1307 Antisense
GAACTGGATGCTCCGTGGATCACAG 146 349 1354 Antisense
Sequence Source Affymetrix Proprietary Database