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[175347_s_at] ABC transporter

Description AV199878_rc /REP_DB=TREMBL Accession /GB=AV199878 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk553a1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 31      6grp_high1_10_10 > 03      4grp_highest_8_8 > 25      4grp_high_8_8 > 60      6grp_highest_nonorm > 02      6grp_total > 24      4grp_total > 60      6grp_highest_sub > De      6grp_cgc > 31      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 5520
1 2 3 4 range
A 4517.2
(1.3)
P 		4570.5
(1.3)
P 		6061.9
(3)
P 		732.6
(-3)
P 		5329
B 4424.9
(1.3)
P 		5116.4
(2.1)
P 		5917.8
(3)
P 		693.4
(-3)
P 		5224
C 4172.2
(1.8)
P 		4891.6
(2.8)
P 		5072.5
(3)
P 		541.8
(-3)
P 		4531
avr 4371.4
(1.4) 		4859.5
(2) 		5684.1
(3) 		655.9
(-3) 		5028

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2491
1 2 3 4 5 6 range
A 2981.1
(2.1)
P 		3271.6
(3)
P 		2407.9
(0.2)
P 		1601.5
(-2.4)
P 		1431.9
(-3)
P 		1438.7
(-3)
P 		1840
B 3855.9
(3)
P 		2951.3
(0.8)
P 		2302
(-0.8)
P 		2045.2
(-1.4)
P 		1425
(-2.9)
P 		1381.2
(-3)
P 		2475
C 3562.1
(3)
P 		2743.9
(0.8)
P 		2573.1
(0.3)
P 		1593.5
(-2.4)
P 		1583.1
(-2.4)
P 		1365.3
(-3)
P 		2197
avr 3466.4
(3) 		2988.9
(1.6) 		2427.7
(-0) 		1746.7
(-2) 		1480
(-2.8) 		1395.1
(-3) 		2071
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1677
1 2 3 4 range
A 1644.7
(3)
P 		992.1
(0.5)
P 		1584.7
(2.8)
P 		107.2
(-3)
P 		1538
B 1411.1
(3)
P 		1263.6
(2.3)
P 		1371.3
(2.8)
P 		147.8
(-3)
P 		1263
C 1381.1
(1.6)
P 		1406.4
(1.7)
P 		1767.9
(3)
P 		91.4
(-3)
P 		1677
avr 1479
(2.6) 		1220.7
(1.5) 		1574.6
(3) 		115.5
(-3) 		1459

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1021
1 2 3 4 5 6 range
A 549.5
(-1.5)
P 		1163.5
(3)
P 		524.4
(-1.7)
P 		406.2
(-2.6)
P 		432.1
(-2.4)
P 		350.3
(-3)
P 		813
B 1341.7
(3)
P 		982.4
(0.4)
P 		559
(-2.7)
P 		541.7
(-2.8)
P 		579
(-2.5)
P 		515
(-3)
P 		827
C 1320.3
(3)
P 		837.2
(0.1)
P 		654.9
(-1)
P 		320.5
(-3)
P 		512.3
(-1.8)
P 		457.1
(-2.2)
P 		1000
avr 1070.5
(3) 		994.4
(2.3) 		579.4
(-1.5) 		422.8
(-3) 		507.8
(-2.2) 		440.8
(-2.8) 		648
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175347_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20449
Sequence Type Exemplar sequence
Representative Public ID AV199878 NCBI
Target Description AV199878_rc /REP_DB=TREMBL Accession /GB=AV199878 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk553a1 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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 10/11 None
GENEFINDER00000040884 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:494308:496070:1 11/11 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:495793-496121(+) 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:175347_S_AT
aatcggaaatcacgaaaccctactgaaggacaccaacggaacctacgcgaagctcgttca
acgccaaatgatgggagatcagaagccacgtaaacggccggcggtcgccagatcgggacc
tcagccagccgcgtcaatcaacgtggcaggaccatcgcagggtaatgcaatgtccctgtt
gtcgacgtctttcagccaatctgccagtagtgttacttctcatta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATCGGAAATCACGAAACCCTACTG 106 161 64 Antisense
GAAACCCTACTGAAGGACACCAACG 547 355 77 Antisense
ACACCAACGGAACCTACGCGAAGCT 601 99 93 Antisense
GCGAAGCTCGTTCAACGCCAAATGA 249 289 110 Antisense
TCAGAAGCCACGTAAACGGCCGGCG 500 611 142 Antisense
CCAGCCGCGTCAATCAACGTGGCAG 588 273 188 Antisense
TCAACGTGGCAGGACCATCGCAGGG 348 629 201 Antisense
GGCAGGACCATCGCAGGGTAATGCA 658 517 208 Antisense
GTAATGCAATGTCCCTGTTGTCGAC 14 463 225 Antisense
GTCTTTCAGCCAATCTGCCAGTAGT 550 467 250 Antisense
CTGCCAGTAGTGTTACTTCTCATTA 690 235 264 Antisense
Sequence Source Affymetrix Proprietary Database