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[191228_at] p-glycoprotein

Description F42E11.1 /REP_DB=WormBase Gene ID /WP=CE03308 /GEN=pgp-4 /TR=Q20331 /GB=CAA91463.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=p-glycoprotein
Cluster 6grp_highest_10_10 > 61      6grp_high1_10_10 > 26      4grp_high_8_8 > 33      6grp_highest_nonorm > 70      6grp_total > 26      4grp_total > 46      6grp_highest_sub > De      6grp_cgc > 14      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 454
1 2 3 4 range
A 544.2
(3)
P 		289.8
(-1.2)
P 		228.6
(-2.2)
P 		180.9
(-3)
M 		363
B 624.4
(3)
P 		254
(-1.9)
P 		224.9
(-2.3)
M 		172.8
(-3)
P 		452
C 626.8
(3)
P 		270.3
(-2)
P 		210
(-2.9)
P 		200.5
(-3)
P 		426
avr 598.5
(3) 		271.4
(-1.7) 		221.2
(-2.5) 		184.7
(-3) 		414

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 246
1 2 3 4 5 6 range
A 415.7
(3)
P 		326.9
(0.5)
P 		217.7
(-2.6)
P 		204.3
(-3)
P 		244.3
(-1.9)
P 		270.2
(-1.1)
P 		211
B 421.9
(3)
P 		362.7
(1.4)
P 		232.1
(-2.2)
P 		206.8
(-2.9)
P 		203.8
(-3)
P 		255.8
(-1.6)
P 		218
C 369
(3)
P 		344.7
(2.2)
P 		261.6
(-0.3)
P 		225.5
(-1.5)
P 		176
(-3)
P 		216.3
(-1.7)
P 		193
avr 402.2
(3) 		344.8
(1.2) 		237.1
(-2.1) 		212.2
(-2.9) 		208
(-3) 		247.4
(-1.8) 		194
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 181
1 2 3 4 range
A 198.2
(3)
P 		62.9
(-1.7)
P 		59.7
(-1.8)
P 		26.5
(-3)
M 		172
B 199.1
(3)
P 		62.7
(-2)
P 		52.1
(-2.4)
M 		36.8
(-3)
P 		162
C 207.5
(3)
P 		77.7
(-1.5)
P 		73.2
(-1.6)
P 		33.8
(-3)
P 		174
avr 201.6
(3) 		67.8
(-1.7) 		61.7
(-2) 		32.4
(-3) 		169

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 102
1 2 3 4 5 6 range
A 76.6
(-0.5)
P 		116.3
(3)
P 		47.4
(-3)
P 		51.8
(-2.6)
P 		73.7
(-0.7)
P 		65.8
(-1.4)
P 		69
B 146.8
(3)
P 		120.7
(1.3)
P 		56.4
(-2.9)
P 		54.8
(-3)
P 		82.8
(-1.2)
P 		95.4
(-0.4)
P 		92
C 136.8
(3)
P 		105.2
(0.9)
P 		66.6
(-1.6)
P 		45.3
(-3)
P 		57
(-2.2)
P 		72.4
(-1.2)
P 		92
avr 120.1
(3) 		114.1
(2.5) 		56.8
(-2.5) 		50.6
(-3) 		71.2
(-1.2) 		77.9
(-0.6) 		70
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191228_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16288
Sequence Type Exemplar sequence
Representative Public ID F42E11.1 NCBI
Target Description F42E11.1 /REP_DB=WormBase Gene ID /WP=CE03308 /GEN=pgp-4 /TR=Q20331 /GB=CAA91463.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=p-glycoprotein
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_077501(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077501 NCBI Caenorhabditis elegans F42E11.1 (p-glycoprotein) mRNA, complete cds. 11/11 None
SNAP00000010139 ENSEMBL cdna:SNAP chromosome:CEL140:X:11358444:11363833:1 11/11 None
GENEFINDER00000010145 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11359092:11363833:1 11/11 None
F42E11.1.2 ENSEMBL cdna:known chromosome:CEL140:X:11359092:11364035:1 gene:F42E11.1 11/11 None
F42E11.1.1 ENSEMBL cdna:known chromosome:CEL140:X:11359092:11363963:1 gene:F42E11.1 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
chrX:11359091-11363833(+) 100.0 100.0
Public Domain and Genome References
Gene Title p-glycoprotein
Gene Symbol pgp-4
Ensembl F42E11.1
Entrez Gene 181327 Entrez gene
SwissProt Q20331 EMBL-EBI
WormBase CE03308 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:259579_AT multidrug resistance P-glycoprotein, putative 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
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 CAA91463 Hypothetical protein F42E11.1 [Caenorhabditis elegans] ref|NP_509902.1| F42E11.1 [Caenorhabditis elegans] 0.0
blast CAE70651 Hypothetical protein CBG17356 [Caenorhabditis briggsae] 0.0
blast CAA91495 Hypothetical protein ZK455.7 [Caenorhabditis elegans] emb|CAA91467.1| Hypothetical protein ZK455.7 [Caenorhabditis elegans] ref|NP_509901.1| P-GlycoProtein related family member (pgp-3) [Caenorhabditis elegans] sp|P34713|MDR3_CAEEL Multidrug resistance protein 3 (P-glycoprotein C) pir||T22094 hypothetical protein ZK455.7 - Caenorhabditis elegans 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001140 EMBL-EBI ABC transporter, transmembrane region 1.0E-63
Pfam IPR001140 EMBL-EBI ABC transporter, transmembrane region 4.8E-59
Pfam IPR003439 EMBL-EBI ABC transporter 1.1E-59
Pfam IPR003439 EMBL-EBI ABC transporter 6.9E-69
Pfam IPR001140 EMBL-EBI ABC transporter, transmembrane region 1.0E-63
Pfam IPR001140 EMBL-EBI ABC transporter, transmembrane region 4.8E-59
Pfam IPR003439 EMBL-EBI ABC transporter 1.1E-59
Pfam IPR003439 EMBL-EBI ABC transporter 6.9E-69
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509902.1 12 42-64,97-119,172-194,198-215,274-296,300-322,706-728,748-770,826-848,853-872,933-955,965-987
F42E11.1.2 12 42-64,97-119,172-194,198-215,274-296,300-322,706-728,748-770,826-848,853-872,933-955,965-987
F42E11.1.1 12 42-64,97-119,172-194,198-215,274-296,300-322,706-728,748-770,826-848,853-872,933-955,965-987
SNAP00000010139 12 57-79,112-134,187-209,213-230,289-311,315-337,721-743,763-785,841-863,868-887,948-970,980-1002
GENEFINDER00000010145 12 42-64,97-119,172-194,198-215,274-296,300-322,706-728,748-770,826-848,853-872,933-955,965-987
Sequence
Target Sequence 
>C. ELEGANS:191228_AT
agacatctctgtcaaacatctccgccacaatattgctcttgttggccaggaacccacact
ttttaatcttactatacgcgagaatattacatatggacttgaaaacgtgtctcaagaaca
agttgaaaaagcagcaaccctggctaacatccatagttttgttgaaaatctaccggaagg
atatgatacttccgttggtgcttctggcggacgattatctggtggccaaaaacaacgtat
tgctattgcaagagcaattgtcagaaatccaaaaattctccttctcgacgaagccacgtc
cgcgctcgatacagaaagtgaaaaaattgtacaggaagctctggataaagcgagacttgg
aagaacttgtgttgttattgctcatcgtctttcaactattcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGACATCTCTGTCAAACATCTCCGC 617 71 3294 Antisense
AAACATCTCCGCCACAATATTGCTC 352 129 3307 Antisense
ATATTGCTCTTGTTGGCCAGGAACC 411 19 3323 Antisense
TGGCCAGGAACCCACACTTTTTAAT 632 543 3336 Antisense
GCAACCCTGGCTAACATCCATAGTT 542 319 3427 Antisense
GATATGATACTTCCGTTGGTGCTTC 533 425 3473 Antisense
TTGGTGCTTCTGGCGGACGATTATC 503 705 3488 Antisense
CCAAAAATTCTCCTTCTCGACGAAG 412 275 3562 Antisense
ACGTCCGCGCTCGATACAGAAAGTG 342 95 3589 Antisense
ACTTGTGTTGTTATTGCTCATCGTC 124 105 3658 Antisense
TGCTCATCGTCTTTCAACTATTCAA 339 581 3672 Antisense
Sequence Source Affymetrix Proprietary Database