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[189322_at] abc transporter

Description F12B6.1 /REP_DB=WormBase Gene ID /WP=CE09356 /TR=O01790 /GB=AAK21369.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=abc transporter
Cluster 6grp_total > 16      4grp_total > 47      6grp_cgc > 13      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 392
1 2 3 4 range
A 628.8
(3)
P 		319.6
(-2.2)
A 		275.1
(-3)
A 		327.3
(-2.1)
P 		354
B 501.1
(3)
P 		284.1
(-1.9)
A 		237.2
(-3)
A 		263.1
(-2.4)
P 		264
C 463.9
(3)
P 		281.2
(-2.3)
A 		256.3
(-3)
P 		297
(-1.8)
P 		208
avr 531.3
(3) 		295
(-2.2) 		256.2
(-3) 		295.8
(-2.1) 		275

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 402
1 2 3 4 5 6 range
A 465.5
(3)
A 		332.9
(-0.4)
P 		242.2
(-2.7)
P 		229.5
(-3)
A 		280.9
(-1.7)
A 		313.7
(-0.9)
P 		236
B 612.7
(3)
P 		440.7
(0.3)
P 		384.9
(-0.6)
P 		270.6
(-2.4)
A 		235.2
(-3)
A 		255.9
(-2.7)
P 		378
C 472.9
(3)
P 		402.7
(1.4)
P 		322.9
(-0.4)
A 		249.7
(-2.1)
A 		210.9
(-3)
A 		303
(-0.9)
P 		262
avr 517
(3) 		392.1
(0.3) 		316.7
(-1.4) 		249.9
(-2.8) 		242.3
(-3) 		290.9
(-1.9) 		275
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 181
1 2 3 4 range
A 229
(3)
P 		69.4
(-2.3)
A 		71.9
(-2.2)
A 		47.9
(-3)
P 		181
B 159.8
(3)
P 		70.2
(-2.1)
A 		55
(-3)
A 		56.1
(-2.9)
P 		105
C 153.6
(3)
P 		80.8
(-1.2)
A 		89.3
(-0.7)
P 		50.1
(-3)
P 		104
avr 180.8
(3) 		73.5
(-2) 		72.1
(-2) 		51.4
(-3) 		129

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 163
1 2 3 4 5 6 range
A 85.8
(0)
A 		118.4
(3)
P 		52.8
(-3)
P 		58.2
(-2.5)
A 		84.8
(-0.1)
A 		76.4
(-0.8)
P 		66
B 213.2
(3)
P 		146.7
(0.2)
P 		93.5
(-2.1)
P 		71.7
(-3)
A 		95.6
(-2)
A 		95.4
(-2)
P 		142
C 175.3
(3)
P 		122.9
(0.5)
P 		82.2
(-1.5)
A 		50.2
(-3)
A 		68.2
(-2.1)
A 		101.4
(-0.5)
P 		125
avr 158.1
(3) 		129.3
(1.2) 		76.2
(-2) 		60
(-3) 		82.9
(-1.6) 		91.1
(-1.1) 		98
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189322_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.229
Sequence Type Exemplar sequence
Representative Public ID F12B6.1 NCBI
Target Description F12B6.1 /REP_DB=WormBase Gene ID /WP=CE09356 /TR=O01790 /GB=AAK21369.1 /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_058548(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058548 NCBI Caenorhabditis elegans ABC Transporter family member (abt-2) (abt-2) mRNA, complete cds. 11/11 None
SNAP00000032176 ENSEMBL cdna:SNAP chromosome:CEL140:I:2254037:2267898:-1 11/11 None
GENEFINDER00000032178 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:2256153:2267898:-1 11/11 None
F12B6.1 ENSEMBL cdna:known chromosome:CEL140:I:2255936:2267884:-1 gene:F12B6.1 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
chrI:2257046-2267884(-) 92.45 100.0
Public Domain and Genome References
Gene Title abc transporter
Gene Symbol abt-2
Ensembl F12B6.1
Entrez Gene 171782 Entrez gene
SwissProt O01790 EMBL-EBI
WormBase CE30511 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:17742_G_AT ABC transporter family protein at
ATGENOME1:18098_AT ABC transporter family protein at
ATGENOME1:17741_AT ABC transporter family protein at
ATH1-121501:260496_AT ABC transporter family protein at
CANINE_2:CFAAFFX.5026.1.S1_S_AT similar to ATP-binding cassette, sub-family A member 1 cfa
CANINE_2:CFAAFFX.5036.1.S1_AT similar to ATP-binding cassette, sub-family A member 1 cfa
CANINE_2:CFAAFFX.5036.1.S1_S_AT similar to ATP-binding cassette, sub-family A member 1 cfa
CHICKEN:GGA.102.1.S1_AT ATP-binding cassette, sub-family A (ABC1), member 1 gga
HG-U95AV2:31998_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A:203505_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133_PLUS_2:203505_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A_2:203505_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133_PLUS_2:203504_S_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A:203504_S_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-FOCUS:203504_S_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A_2:203504_S_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HU35KSUBA:RC_AA521292_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HU35KSUBA:AA292158_S_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HU35KSUBD:RC_AA434152_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133_PLUS_2:216066_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A_2:216066_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A:216066_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
U133_X3P:G9755158_3P_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
U133_X3P:G5915657_3P_A_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
U133_X3P:HS.211562.1.S1_3P_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U95AV2:31999_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U95AV2:32000_G_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U95B:52656_S_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U95C:60496_R_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U95E:78250_F_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U95E:78253_R_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133_PLUS_2:215869_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A_2:215869_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A:215869_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133_PLUS_2:1570279_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
U133_X3P:HS2.407188.1.S1_3P_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
U133_X3P:HS.288451.0.S1_3P_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133_PLUS_2:1565776_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133_PLUS_2:1565777_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133_PLUS_2:215876_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A_2:215876_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
HG-U133A:215876_AT ATP-binding cassette, sub-family A (ABC1), member 1 hs
MU11KSUBA:AA690738_S_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MU11KSUBB:X75926_S_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MG-U74AV2:97198_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MG-U74AV2:94354_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOE430A:1421840_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOUSE430A_2:1421840_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOUSE430_2:1421840_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOE430A:1450392_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOUSE430A_2:1450392_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOUSE430_2:1450392_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOE430A:1421839_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOUSE430A_2:1421839_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
MOUSE430_2:1421839_AT ATP-binding cassette, sub-family A (ABC1), member 1 mm
RG-U34C:RC_AI171534_AT hypothetical gene supported by NM_178095 rn
RAE230B:1383355_AT hypothetical gene supported by NM_178095 rn
RAT230_2:1383355_AT hypothetical gene supported by NM_178095 rn
RAE230B:1384381_AT hypothetical gene supported by NM_178095 rn
RAT230_2:1384381_AT hypothetical gene supported by NM_178095 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
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 AAK21369 Abc transporter family protein 2 [Caenorhabditis elegans] ref|NP_490949.2| ABC Transporter family member (abt-2) [Caenorhabditis elegans] 0.0
blast T15200 hypothetical protein F12B6.1 - Caenorhabditis elegans 0.0
blast CAE60304 Hypothetical protein CBG03891 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003439 EMBL-EBI ABC transporter 5.2E-61
Pfam IPR003439 EMBL-EBI ABC transporter 5.4E-51
Pfam IPR003439 EMBL-EBI ABC transporter 5.2E-61
Pfam IPR003439 EMBL-EBI ABC transporter 5.4E-51
Pfam IPR003439 EMBL-EBI ABC transporter 5.2E-61
Pfam IPR003439 EMBL-EBI ABC transporter 5.4E-51
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_490949.2 12 85-107,127-149,164-186,191-210,260-282,571-593,923-945,966-988,1003-1025,1032-1054,1069-1091,1131-1153
F12B6.1 12 85-107,127-149,164-186,191-210,260-282,571-593,923-945,966-988,1003-1025,1032-1054,1069-1091,1131-1153
SNAP00000032176 13 85-107,132-154,166-185,190-209,222-244,259-281,586-608,938-960,981-1003,1018-1040,1047-1069,1084-1106,1146-1168
GENEFINDER00000032178 12 74-96,116-138,153-175,180-199,249-271,576-598,928-950,971-993,1008-1030,1037-1059,1074-1096,1136-1158
Sequence
Target Sequence 
>C. ELEGANS:189322_AT
ctcaattcgacgctctcaacatgaagctgagtaccagggagaacttgaagttctacgcga
ggattcgaggaattgtaccgactcaaatcgattcgataatcgatcgtctgctgattgctc
tccacctccgtccctacgcaaacacccagacgtcaagcctctccggtggaaatcgacgaa
aactctctgtcgcagtggcgctggtcagtcagccatctctgatcttcctcgacgaaccat
cagctggaatggatccaggatctcaacaattcctttggaaggttattgaaagactttgta
aatctggaaaagcagtagtcctaacctcacattcaatggaagagtgtgaagctttgtgta
ctagaattgcaattatggatcgtggaagaatcaggtgtcttggaggaaagcagcatctga
aatccaagtatggaaagggttcaatgttgacaatgaagatgggaaaagatgagaatgcca
aggaaatcgccgggattatgagatcaaaacttggcgatggctcgagagtcgaggcgattc
attgctccacgatttttattcacattga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCAATTCGACGCTCTCAACATGAA 270 227 3737 Antisense
TAATCGATCGTCTGCTGATTGCTCT 631 635 3833 Antisense
CTACGCAAACACCCAGACGTCAAGC 707 225 3870 Antisense
TCAAGCCTCTCCGGTGGAAATCGAC 269 631 3889 Antisense
GACGAAAACTCTCTGTCGCAGTGGC 457 375 3911 Antisense
CTGATCTTCCTCGACGAACCATCAG 104 237 3955 Antisense
GGATCCAGGATCTCAACAATTCCTT 254 513 3987 Antisense
GTAGTCCTAACCTCACATTCAATGG 218 423 4051 Antisense
AACTTGGCGATGGCTCGAGAGTCGA 660 137 4244 Antisense
GAGAGTCGAGGCGATTCATTGCTCC 142 395 4260 Antisense
GCTCCACGATTTTTATTCACATTGA 700 297 4280 Antisense
Sequence Source Affymetrix Proprietary Database