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[189262_at] ABC transporter

Description W04C9.1 /REP_DB=WormBase Gene ID /WP=CE28355 /TR=Q9TZD9 /GB=AAC68724.2 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ABC transporter
Cluster 6grp_highest_10_10 > 31      6grp_high1_10_10 > 03      4grp_highest_8_8 > 16      4grp_high_8_8 > 60      6grp_highest_nonorm > 41      6grp_total > 24      4grp_total > 59      6grp_highest_sub > De      6grp_cgc > 33      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1670
1 2 3 4 range
A 1259.3
(1.8)
P 		1443.4
(2.6)
P 		1534.2
(3)
P 		176.2
(-3)
P 		1358
B 1308.6
(1.3)
P 		1573.3
(2.3)
P 		1764.9
(3)
P 		183.8
(-3)
P 		1581
C 1260.3
(1)
P 		1727.4
(2.7)
P 		1811.1
(3)
P 		141.1
(-3)
P 		1670
avr 1276.1
(1.3) 		1581.4
(2.5) 		1703.4
(3) 		167
(-3) 		1536

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 802
1 2 3 4 5 6 range
A 1110.7
(3)
P 		1081.3
(2.8)
P 		820.7
(0.7)
P 		478
(-1.9)
P 		443
(-2.2)
P 		341.8
(-3)
P 		769
B 1005.7
(2.8)
P 		934.8
(2.2)
P 		1021
(3)
P 		549.3
(-1.6)
P 		412.1
(-3)
P 		425.5
(-2.9)
P 		609
C 1144
(3)
P 		884.3
(0.9)
P 		696
(-0.7)
P 		416.3
(-3)
P 		518
(-2.2)
P 		464.6
(-2.6)
P 		728
avr 1086.8
(3) 		966.8
(1.9) 		845.9
(0.9) 		481.2
(-2.4) 		457.7
(-2.6) 		410.6
(-3) 		676
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 607
1 2 3 4 range
A 458.5
(3)
P 		313.3
(1)
P 		401.1
(2.2)
P 		25.8
(-3)
P 		433
B 417.3
(3)
P 		388.6
(2.5)
P 		409
(2.9)
P 		39.2
(-3)
P 		378
C 417.2
(0.9)
P 		496.6
(1.7)
P 		631.2
(3)
P 		23.8
(-3)
P 		607
avr 431
(2.3) 		399.5
(1.9) 		480.4
(3) 		29.6
(-3) 		451

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 341
1 2 3 4 5 6 range
A 204.8
(-0.6)
P 		384.5
(3)
P 		178.7
(-1.1)
P 		121.2
(-2.2)
P 		133.7
(-2)
P 		83.2
(-3)
P 		301
B 349.9
(3)
P 		311.1
(1.9)
P 		247.9
(0)
P 		145.5
(-3)
P 		167.4
(-2.4)
P 		158.7
(-2.6)
P 		204
C 424
(3)
P 		269.8
(0.3)
P 		177.1
(-1.4)
P 		83.7
(-3)
P 		167.6
(-1.5)
P 		155.5
(-1.7)
P 		340
avr 326.2
(3) 		321.8
(2.9) 		201.2
(-0.6) 		116.8
(-3) 		156.2
(-1.9) 		132.5
(-2.6) 		209
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189262_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2559
Sequence Type Exemplar sequence
Representative Public ID W04C9.1 NCBI
Target Description W04C9.1 /REP_DB=WormBase Gene ID /WP=CE28355 /TR=Q9TZD9 /GB=AAC68724.2 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ABC transporter
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_001026495(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001026495 NCBI Caenorhabditis elegans HAlF transporter (PGP related) family member (haf-4) (haf-4) mRNA, complete cds. 11/11 None
SNAP00000040873 ENSEMBL cdna:SNAP chromosome:CEL140:I:494263:501731:1 11/11 None
GENEFINDER00000040884 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:494308:496070:1 10/11 None
W04C9.1 ENSEMBL cdna:known chromosome:CEL140:I:489987:496157:1 gene:W04C9.1 11/11 A 
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
chrI:490053-496070(+) 100.0 100.0
Public Domain and Genome References
Gene Title ABC transporter
Gene Symbol haf-4
Ensembl W04C9.1
Entrez Gene 171639 Entrez gene
SwissProt Q9TZD9 EMBL-EBI
WormBase CE28355 Wormbase
Functional Annotations
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
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
166 nucleotide binding inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC68724 Half transporter (pgp related) protein 4 [Caenorhabditis elegans] ref|NP_001021666.1| HAlF transporter (PGP related) family member (haf-4) [Caenorhabditis elegans] 0.0
blast CAE74830 Hypothetical protein CBG22668 [Caenorhabditis briggsae] 0.0
blast AAK39394 Half transporter (pgp related) protein 9, isoform a [Caenorhabditis elegans] ref|NP_491754.1| HAlF transporter (PGP related) family member (haf-9) [Caenorhabditis elegans] 0.0
blast AAC68724 Half transporter (pgp related) protein 4 [Caenorhabditis elegans] ref|NP_001021666.1| HAlF transporter (PGP related) family member (haf-4) [Caenorhabditis elegans] 1.0E-103
blast CAE74830 Hypothetical protein CBG22668 [Caenorhabditis briggsae] 7.0E-99
blast AAC68724 Half transporter (pgp related) protein 4 [Caenorhabditis elegans] ref|NP_001021666.1| HAlF transporter (PGP related) family member (haf-4) [Caenorhabditis elegans] 5.0E-96
blast CAE74830 Hypothetical protein CBG22668 [Caenorhabditis briggsae] 4.0E-91
Protein Domains
Database ID Description E-Value
Pfam IPR003439 EMBL-EBI ABC transporter 1.1E-39
Pfam IPR003439 EMBL-EBI ABC transporter 8.0E-35
Pfam IPR001140 EMBL-EBI ABC transporter, transmembrane region 8.6E-44
Pfam IPR003439 EMBL-EBI ABC transporter 5.1E-59
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001021666.1 9 7-29,44-66,87-106,116-138,180-202,222-244,294-316,320-342,404-426
W04C9.1 9 7-29,44-66,87-106,116-138,180-202,222-244,294-316,320-342,404-426
Sequence
Target Sequence 
>C. ELEGANS:189262_AT
ctgttcgctcgttctgtgatggaaaatgtcagatacggtgtcgaagtggcggatacggaa
atcattcgctcttgtgaaatggcgaatgctcacggattcattatgcaaaccacgttgaaa
tacgaaacaaacgtcggagagaagggaacacaaatgtccggtggtcagaagcaacgtatc
gcaattgctcgtgctcttgttcgtgagccagcgattctcttgttggatgaagccacgtcg
gcgttggacaccgagtccgaacatcttgttcaggaagcgatttataagaatttggatgga
aagagtgtcattttgattgcacatcga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTGTTCGCTCGTTCTGTGATGGAAA 371 239 1765 Antisense
GATACGGTGTCGAAGTGGCGGATAC 242 423 1796 Antisense
GATACGGAAATCATTCGCTCTTGTG 141 423 1816 Antisense
AATGGCGAATGCTCACGGATTCATT 222 161 1842 Antisense
CGGATTCATTATGCAAACCACGTTG 386 243 1857 Antisense
ATGTCCGGTGGTCAGAAGCAACGTA 173 49 1918 Antisense
AGCAACGTATCGCAATTGCTCGTGC 598 75 1934 Antisense
CTCGTGCTCTTGTTCGTGAGCCAGC 216 229 1952 Antisense
GAGCCAGCGATTCTCTTGTTGGATG 387 385 1969 Antisense
GGCGTTGGACACCGAGTCCGAACAT 408 539 2004 Antisense
GAGTGTCATTTTGATTGCACATCGA 515 401 2067 Antisense
Sequence Source Affymetrix Proprietary Database