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[191455_s_at] abc transporter

Description C34G6.4 /REP_DB=WormBase Gene ID /WP=CE08576 /GEN=pgp-2 /TR=O01495 /GB=AAB52482.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=abc transporter
Cluster 6grp_highest_10_10 > 17      6grp_high1_10_10 > 71      4grp_highest_8_8 > 26      4grp_high_8_8 > 59      6grp_highest_nonorm > 72      6grp_total > 71      4grp_total > 60      6grp_highest_sub > 04      6grp_cgc > 84      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 200
1 2 3 4 range
A 326.4
(3)
P 		280.6
(0.2)
P 		257
(-1.3)
P 		229.5
(-3)
P 		97
B 284.8
(-0.9)
P 		316.2
(0.2)
P 		398.7
(3)
P 		223.5
(-3)
P 		175
C 337.6
(0.3)
P 		328.7
(0.1)
P 		423.4
(3)
P 		229.2
(-3)
P 		194
avr 316.3
(1) 		308.5
(0.7) 		359.7
(3) 		227.4
(-3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 256
1 2 3 4 5 6 range
A 285.6
(-3)
P 		401.4
(0.4)
P 		423.7
(1)
P 		492.1
(3)
P 		415.2
(0.8)
P 		288.8
(-2.9)
P 		207
B 385.7
(-2.6)
P 		400.6
(-2.1)
P 		529.6
(2.6)
P 		541.3
(3)
P 		390.9
(-2.5)
P 		375.9
(-3)
P 		165
C 344.5
(-3)
P 		424.1
(-0.1)
P 		437.7
(0.3)
P 		511.6
(3)
P 		441.2
(0.5)
P 		354.9
(-2.6)
P 		167
avr 338.6
(-3) 		408.7
(-0.6) 		463.7
(1.3) 		515
(3) 		415.8
(-0.4) 		339.9
(-3) 		176
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 114
1 2 3 4 range
A 118.9
(3)
P 		60.9
(-1.1)
P 		67.2
(-0.6)
P 		33.6
(-3)
P 		85
B 90.8
(2.8)
P 		78.1
(1.1)
P 		92.4
(3)
P 		47.6
(-3)
P 		45
C 111.7
(1)
P 		94.5
(0.1)
P 		147.6
(3)
P 		38.6
(-3)
P 		109
avr 107.1
(3) 		77.8
(0.4) 		102.4
(2.6) 		39.9
(-3) 		67

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 106
1 2 3 4 5 6 range
A 52.6
(-3)
P 		142.8
(3)
P 		92.3
(-0.4)
P 		124.8
(1.8)
P 		125.3
(1.8)
P 		70.3
(-1.8)
P 		90
B 134.2
(-1.9)
P 		133.4
(-2)
P 		128.6
(-3)
P 		143.4
(-0.1)
P 		158.8
(3)
P 		140.2
(-0.7)
P 		30
C 127.7
(0.7)
P 		129.4
(1)
P 		111.4
(-1.7)
P 		102.9
(-3)
P 		142.8
(3)
P 		118.8
(-0.6)
P 		40
avr 104.8
(-3) 		135.2
(1.9) 		110.8
(-2) 		123.7
(0) 		142.3
(3) 		109.8
(-2.2) 		38
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191455_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2002
Sequence Type Exemplar sequence
Representative Public ID C34G6.4 NCBI
Target Description C34G6.4 /REP_DB=WormBase Gene ID /WP=CE08576 /GEN=pgp-2 /TR=O01495 /GB=AAB52482.1 /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_059306(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059306 NCBI Caenorhabditis elegans P-GlycoProtein related family member (pgp-2) (pgp-2) mRNA, complete cds. 11/11 None
SNAP00000014375 ENSEMBL cdna:SNAP chromosome:CEL140:I:5897000:5903772:1 11/11 None
GENEFINDER00000014383 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5897000:5904005:1 11/11 None
C34G6.4 ENSEMBL cdna:known chromosome:CEL140:I:5897000:5904075:1 gene:C34G6.4 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
chrI:5896999-5903772(+) 100.0 100.0
Public Domain and Genome References
Gene Title abc transporter
Gene Symbol pgp-2
Ensembl C34G6.4
Entrez Gene 172262 Entrez gene
SwissProt O01495 EMBL-EBI
WormBase CE29212 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:251248_AT multidrug resistant (MDR) ABC transporter, putative at
DROSOPHILA_2:1638775_AT Multi drug resistance 50 dm
DROSGENOME1:143589_AT Multi drug resistance 50 dm
MG-U74AV2:93414_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B mm
MOUSE430_2:1418872_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B mm
MOE430A:1418872_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B mm
MOUSE430A_2:1418872_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B mm
MU11KSUBA:M14757_S_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B mm
MOE430B:1446701_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B mm
MOUSE430_2:1446701_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B mm
MG-U74CV2:134407_F_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B (Abcb1b), mRNA mm
MOUSE430_2:1449594_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B (Abcb1b), mRNA mm
MOE430A:1449594_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B (Abcb1b), mRNA mm
MOUSE430A_2:1449594_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B (Abcb1b), mRNA mm
MG-U74AV2:94798_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B (Abcb1b), mRNA mm
MU11KSUBA:AA185049_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B (Abcb1b), mRNA mm
MU19KSUBA:TC21639_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1B (Abcb1b), mRNA mm
RAE230A:1370583_S_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1 rn
RAT230_2:1370583_S_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1 rn
RT-U34:M81855_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1 rn
RG-U34A:M81855_AT ATP-binding cassette, sub-family B (MDR/TAP), member 1 rn
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 AAB52482 P-glycoprotein related protein 2 [Caenorhabditis elegans] ref|NP_491707.1| P-GlycoProtein related family member (pgp-2) [Caenorhabditis elegans] 0.0
blast CAE60408 Hypothetical protein CBG04013 [Caenorhabditis briggsae] 0.0
blast AAC38987 P-glycoprotein [Haemonchus contortus] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001140 EMBL-EBI ABC transporter, transmembrane region 1.7E-57
Pfam IPR001140 EMBL-EBI ABC transporter, transmembrane region 1.3E-50
Pfam IPR003439 EMBL-EBI ABC transporter 6.5E-66
Pfam IPR003439 EMBL-EBI ABC transporter 4.7E-61
Pfam IPR001140 EMBL-EBI ABC transporter, transmembrane region 1.3E-50
Pfam IPR003439 EMBL-EBI ABC transporter 4.7E-61
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491707.1 11 47-69,113-135,189-208,212-229,293-315,330-352,698-720,740-759,815-837,841-863,925-947
C34G6.4 11 47-69,113-135,189-208,212-229,293-315,330-352,698-720,740-759,815-837,841-863,925-947
SNAP00000014375 11 47-69,113-135,189-208,212-229,293-315,330-352,698-720,740-759,815-837,841-863,925-947
GENEFINDER00000014383 11 47-69,113-135,189-208,212-229,293-315,330-352,722-744,764-783,839-861,865-887,949-971
Sequence
Target Sequence 
>C. ELEGANS:191455_S_AT
atgggactgctggagagattctataatcaagataaaggaatgattatgattgatggtgat
aacatccgtaacctaaacatcagttcacttcgcgaacaagtatgtattgtaagtcaagag
ccaacgttgtttgattgcacaattggagaaaatatttgctacggaacaaatcgaaatgtt
acatatcaagaaattgttgaagctgccaaaatggcaaatattcacaatttcattctagga
ttgccagatggttatgatactcatgtcggagagaaaggaactcaactttcgggtggtcaa
aaacaaagaattgccattgcacgggcacttgttcgatctccttctgttttacttttggat
gaagcaactagtgcattagatacggaaagtgaaaagattgtacaagaagcattggacgcc
gcaaaacaaggtcgcacgtgtcttgtcattgctcatcggttgagcacaattcaaaatagt
gacgtcattgcgatcgtcagtgaggg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGGGACTGCTGGAGAGATTCTATA 543 49 3280 Antisense
GTGATAACATCCGTAACCTAAACAT 643 471 3335 Antisense
ACCTAAACATCAGTTCACTTCGCGA 436 87 3350 Antisense
AGAGCCAACGTTGTTTGATTGCACA 239 57 3396 Antisense
CATTGCACGGGCACTTGTTCGATCT 382 215 3594 Antisense
GATCTCCTTCTGTTTTACTTTTGGA 487 419 3614 Antisense
TGTACAAGAAGCATTGGACGCCGCA 332 559 3678 Antisense
GGACGCCGCAAAACAAGGTCGCACG 447 523 3693 Antisense
CAAGGTCGCACGTGTCTTGTCATTG 89 183 3706 Antisense
GTCTTGTCATTGCTCATCGGTTGAG 49 469 3719 Antisense
ACGTCATTGCGATCGTCAGTGAGGG 629 93 3761 Antisense
Sequence Source Affymetrix Proprietary Database