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[192400_at] Ion transport proteins

Description Y54G9A.3 /REP_DB=WormBase Gene ID /WP=CE19231 /GEN=kqt-3 /TR=Q9XWG9 /GB=CAA21699.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Ion transport proteins
Cluster 6grp_total > 27      4grp_total > 39      6grp_cgc > 05      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 119
1 2 3 4 range
A 147.6
(3)
A 		53.4
(-1.9)
A 		48.4
(-2.2)
A 		32.1
(-3)
A 		116
B 149.4
(2.8)
A 		98.9
(-3)
A 		104.7
(-2.3)
A 		150.7
(3)
A 		52
C 132.9
(1.9)
A 		113.7
(-1.7)
A 		106.3
(-3)
A 		139.2
(3)
A 		33
avr 143.3
(3) 		88.7
(-2.8) 		86.5
(-3) 		107.3
(-0.8) 		57

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 102
1 2 3 4 5 6 range
A 127.7
(3)
A 		107.2
(1.8)
A 		116.4
(2.3)
A 		26.1
(-3)
A 		69.5
(-0.4)
A 		87.1
(0.6)
A 		102
B 125.7
(3)
A 		87.4
(-0.5)
A 		88.6
(-0.4)
A 		78.8
(-1.3)
A 		60.5
(-3)
A 		110.5
(1.6)
A 		65
C 123.9
(3)
A 		104.2
(1.1)
A 		61.5
(-3)
A 		79.1
(-1.3)
A 		91.3
(-0.1)
A 		65.4
(-2.6)
A 		62
avr 125.8
(3) 		99.6
(0.6) 		88.8
(-0.4) 		61.3
(-3) 		73.8
(-1.8) 		87.7
(-0.5) 		65
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 53.7
(3)
A 		11.6
(-2.2)
A 		12.6
(-2)
A 		4.7
(-3)
A 		49
B 47.6
(3)
A 		24.4
(-3)
A 		24.3
(-3)
A 		32.1
(-1)
A 		23
C 44
(3)
A 		32.7
(-0.3)
A 		37
(1)
A 		23.5
(-3)
A 		21
avr 48.4
(3) 		22.9
(-2.4) 		24.6
(-2) 		20.1
(-3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 39
1 2 3 4 5 6 range
A 23.5
(0.2)
A 		38.1
(3)
A 		25.4
(0.6)
A 		6.6
(-3)
A 		21
(-0.3)
A 		21.2
(-0.2)
A 		32
B 43.7
(3)
A 		29.1
(-0.8)
A 		21.5
(-2.8)
A 		20.9
(-3)
A 		24.6
(-2)
A 		41.2
(2.3)
A 		23
C 45.9
(3)
A 		31.8
(0.2)
A 		15.6
(-3)
A 		15.9
(-2.9)
A 		29.6
(-0.2)
A 		21.9
(-1.8)
A 		30
avr 37.7
(3) 		33
(1.8) 		20.8
(-1.4) 		14.5
(-3) 		25.1
(-0.3) 		28.1
(0.5) 		23
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192400_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2646
Sequence Type Exemplar sequence
Representative Public ID Y54G9A.3 NCBI
Target Description Y54G9A.3 /REP_DB=WormBase Gene ID /WP=CE19231 /GEN=kqt-3 /TR=Q9XWG9 /GB=CAA21699.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Ion transport proteins
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_064474(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064474 NCBI Caenorhabditis elegans potassium channel, KvQLT family member (kqt-3) (kqt-3) mRNA, complete cds. 11/11 None
GENEFINDER00000011615 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:13708349:13712641:1 11/11 None
Y54G9A.3 ENSEMBL cdna:known chromosome:CEL140:II:13696243:13712793:1 gene:Y54G9A.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000011604 4/11 Cross Hyb Matching Probes None
SNAP00000011605 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:13708393-13712638(+) 100.0 100.0
Public Domain and Genome References
Gene Title Ion transport proteins
Gene Symbol kqt-3
Ensembl Y54G9A.3
Entrez Gene 191699 Entrez gene
SwissProt Q9XWG9 EMBL-EBI
WormBase CE32760 Wormbase
Functional Annotations
Ortholog
ID Title Organism
HG-U95AV2:32077_S_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133A:204487_S_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133_PLUS_2:204487_S_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-FOCUS:204487_S_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133A_2:204487_S_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133_PLUS_2:211217_S_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133A_2:211217_S_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133A:211217_S_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HUGENEFL:U40990_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HUGENEFL:AF003743_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
U133_X3P:G4557688_3P_A_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
U133_X3P:G2961248_3P_A_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U95AV2:40527_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133_PLUS_2:204486_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133A_2:204486_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
HG-U133A:204486_AT potassium voltage-gated channel, KQT-like subfamily, member 1 hs
MOE430A:1449464_AT potassium voltage-gated channel, subfamily Q, member 1 mm
MOUSE430A_2:1449464_AT potassium voltage-gated channel, subfamily Q, member 1 mm
MOUSE430_2:1449464_AT potassium voltage-gated channel, subfamily Q, member 1 mm
MU11KSUBA:U70068_S_AT potassium voltage-gated channel, subfamily Q, member 1 mm
MG-U74AV2:99322_AT potassium voltage-gated channel, subfamily Q, member 1 mm
MG-U74AV2:161796_R_AT potassium voltage-gated channel, subfamily Q, member 1 mm
MOE430B:1446255_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MOUSE430_2:1446255_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MG-U74CV2:130605_R_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MG-U74CV2:131645_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MG-U74CV2:135678_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MOE430B:1442029_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MOUSE430_2:1442029_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MOE430B:1447418_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MOUSE430_2:1447418_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MOE430B:1459443_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
MOUSE430_2:1459443_AT KCNQ1b mRNA for Q1-type potassium channel spliced variant mm
RG-U34A:U92655_AT potassium voltage-gated channel, subfamily Q, member 1 rn
RN-U34:U92655_AT potassium voltage-gated channel, subfamily Q, member 1 rn
RAE230A:1368371_AT potassium voltage-gated channel, subfamily Q, member 1 rn
RAT230_2:1368371_AT potassium voltage-gated channel, subfamily Q, member 1 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6811 ion transport inferred from electronic annotation QuickGO AmiGO
6813 potassium ion transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
8076 voltage-gated potassium channel complex inferred from electronic annotation QuickGO AmiGO
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5216 ion channel activity inferred from electronic annotation QuickGO AmiGO
5249 voltage-gated potassium channel activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA21699 Hypothetical protein Y54G9A.3 [Caenorhabditis elegans] ref|NP_496875.2| potassium channel, KvQLT family member (kqt-3) [Caenorhabditis elegans] 0.0
blast AAT77228 KQT-3 potassium channel [Caenorhabditis elegans] 0.0
blast CAE73306 Hypothetical protein CBG20733 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005821 EMBL-EBI Ion transport protein 4.0E-34
Pfam IPR003937 EMBL-EBI KCNQ voltage-gated potassium channel 1.9E-44
Pfam IPR005821 EMBL-EBI Ion transport protein 4.0E-34
Pfam IPR003937 EMBL-EBI KCNQ voltage-gated potassium channel 1.9E-44
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496875.2 6 77-99,109-131,151-173,217-236,256-278,288-307
Y54G9A.3 6 77-99,109-131,151-173,217-236,256-278,288-307
GENEFINDER00000011615 6 36-58,68-90,110-132,176-195,215-237,247-266
Sequence
Target Sequence 
>C. ELEGANS:192400_AT
aaaagcggatctaccgagtcggcgcggatatagaaatcgattatgagaccgaggagccga
cgactccgacaaggcctcaagggcatatcagtcacgtttgtgagctcacagatgctcatc
gaaacgcgattcgggcgattcgacgggttaagtattttgtggcgaggagaagattccagc
aggcacggaaaccgtatgatgtacgggatgtcattgagcagtactctcaggggcatttga
atatgatggttaggattaaggaactgcagaggagactcgaccaaaccctcggaaaaccgg
gtcagtacgacgggaaagggtcgcggaagggacatcctgtgacaattggttccagactgt
cgcgtctcgaattacagatgtcaagcctcgaccgaaaagtggagtctagtaaccgaacac
tgaacgctctctatcgcctaatggccgaccggaactcgctgacgatatctccatcaccgc
cggcactgataagtaggccagtgtcgcctgccgcctgcctatcaccacgagatcaactct
c

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAAGCGGATCTACCGAGTCGGCGC 489 131 1361 Antisense
TATGAGACCGAGGAGCCGACGACTC 237 655 1402 Antisense
GACTCCGACAAGGCCTCAAGGGCAT 375 371 1422 Antisense
GAAACGCGATTCGGGCGATTCGACG 503 357 1481 Antisense
GGTCGCGGAAGGGACATCCTGTGAC 87 503 1679 Antisense
ACAATTGGTTCCAGACTGTCGCGTC 555 113 1702 Antisense
TACAGATGTCAAGCCTCGACCGAAA 1 641 1733 Antisense
AGTAACCGAACACTGAACGCTCTCT 628 59 1768 Antisense
GAACTCGCTGACGATATCTCCATCA 578 347 1812 Antisense
GATAAGTAGGCCAGTGTCGCCTGCC 584 419 1848 Antisense
GCCTATCACCACGAGATCAACTCTC 616 281 1877 Antisense
Sequence Source Affymetrix Proprietary Database