[Home] | [Total List]

[189473_at] ABC transporter

Description Y39D8C.1 /REP_DB=WormBase Gene ID /WP=CE20234 /TR=Q9TXV8 /GB=AAC69223.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ABC transporter
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 26      4grp_highest_8_8 > 49      4grp_high_8_8 > 41      6grp_highest_nonorm > 70      6grp_total > 16      4grp_total > 54      6grp_highest_sub > De      6grp_cgc > 14      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 347
1 2 3 4 range
A 450.7
(3)
P 		276.5
(-0.6)
P 		242.4
(-1.3)
P 		160.2
(-3)
P 		291
B 380.1
(3)
P 		260.8
(0.4)
P 		257.1
(0.3)
P 		103.3
(-3)
P 		277
C 337.6
(3)
P 		253.8
(-1.1)
P 		246
(-1.5)
P 		214.7
(-3)
P 		123
avr 389.5
(3) 		263.7
(-0.3) 		248.5
(-0.7) 		159.4
(-3) 		230

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 246
1 2 3 4 5 6 range
A 417.8
(3)
P 		326.6
(0.8)
P 		172.9
(-3)
P 		172
(-3)
P 		204.5
(-2.2)
P 		278.3
(-0.4)
P 		246
B 364.1
(2.5)
P 		380.5
(3)
P 		253.7
(-0.7)
P 		186.5
(-2.6)
P 		172.2
(-3)
P 		172.7
(-3)
P 		208
C 398.4
(3)
P 		328.1
(1.1)
P 		232
(-1.4)
P 		188.9
(-2.6)
P 		225.9
(-1.6)
P 		173.4
(-3)
P 		225
avr 393.4
(3) 		345.1
(1.6) 		219.5
(-1.9) 		182.5
(-3) 		200.9
(-2.5) 		208.1
(-2.3) 		211
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 142
1 2 3 4 range
A 164.1
(3)
P 		60
(-1.4)
P 		63.4
(-1.3)
P 		23.4
(-3)
P 		141
B 121.2
(3)
P 		64.4
(-0.4)
P 		59.6
(-0.7)
P 		22
(-3)
P 		99
C 111.7
(3)
P 		73
(-0.1)
P 		85.7
(0.9)
P 		36.2
(-3)
P 		76
avr 132.3
(3) 		65.8
(-0.8) 		69.6
(-0.6) 		27.2
(-3) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 110
1 2 3 4 5 6 range
A 77
(0)
P 		116.2
(3)
P 		37.6
(-3)
P 		43.6
(-2.5)
P 		61.7
(-1.2)
P 		67.8
(-0.7)
P 		79
B 126.7
(3)
P 		126.7
(3)
P 		61.6
(-2.1)
P 		49.4
(-3)
P 		70
(-1.4)
P 		64.4
(-1.8)
P 		77
C 147.7
(3)
P 		100.1
(0.4)
P 		59.1
(-1.8)
P 		38
(-3)
P 		73.1
(-1.1)
P 		58
(-1.9)
P 		110
avr 117.1
(3) 		114.3
(2.8) 		52.8
(-2.3) 		43.7
(-3) 		68.3
(-1) 		63.4
(-1.4) 		73
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189473_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15423
Sequence Type Exemplar sequence
Representative Public ID Y39D8C.1 NCBI
Target Description Y39D8C.1 /REP_DB=WormBase Gene ID /WP=CE20234 /TR=Q9TXV8 /GB=AAC69223.1 /SUBMIT=ST.LOUIS /CHR=5 /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_070774(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070774 NCBI Caenorhabditis elegans ABC Transporter family member (abt-4) (abt-4) mRNA, complete cds. 11/11 None
Y39D8C.1 ENSEMBL cdna:known chromosome:CEL140:V:323626:330553:-1 gene:Y39D8C.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
chrV:323738-330553(-) 100.0 100.0
Public Domain and Genome References
Gene Title ABC transporter
Gene Symbol abt-4
Ensembl Y39D8C.1
Entrez Gene 178559 Entrez gene
SwissProt Q9TXV8 EMBL-EBI
WormBase CE20234 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.29630.1.S1_S_AT similar to ATP-binding cassette, sub-family A member 3 cfa
DROSOPHILA_2:1641152_AT dm
DROSGENOME1:145471_AT dm
CHICKEN:GGA.7294.1.S1_AT similar to ATP-binding cassette, sub-family A member 3; ATP-binding cassette 3; ABC transporter 3 gga
CHICKEN:GGA.7294.2.S1_AT similar to ATP-binding cassette, sub-family A member 3; ATP-binding cassette 3; ABC transporter 3 gga
CHICKEN:GGAAFFX.25344.1.S1_S_AT similar to ATP-binding cassette, sub-family A member 3; ATP-binding cassette 3; ABC transporter 3 gga
CHICKEN:GGAAFFX.25344.3.S1_S_AT similar to ATP-binding cassette, sub-family A member 3; ATP-binding cassette 3; ABC transporter 3 gga
CHICKEN:GGAAFFX.25344.4.S1_S_AT similar to ATP-binding cassette, sub-family A member 3; ATP-binding cassette 3; ABC transporter 3 gga
HG-U133_PLUS_2:204343_AT ATP-binding cassette, sub-family A (ABC1), member 3 hs
HG-U133A:204343_AT ATP-binding cassette, sub-family A (ABC1), member 3 hs
HG-FOCUS:204343_AT ATP-binding cassette, sub-family A (ABC1), member 3 hs
HG-U133A_2:204343_AT ATP-binding cassette, sub-family A (ABC1), member 3 hs
HUGENEFL:U78735_AT ATP-binding cassette, sub-family A (ABC1), member 3 hs
U133_X3P:G4501848_3P_AT ATP-binding cassette, sub-family A (ABC1), member 3 hs
HG-U95AV2:35183_AT ATP-binding cassette, sub-family A (ABC1), member 3 hs
MOUSE430_2:1451869_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MOUSE430A_2:1451869_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MOE430A:1451869_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MG-U74BV2:116635_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MG-U74CV2:135154_R_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MG-U74CV2:134712_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MOE430A:1451731_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MOUSE430A_2:1451731_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MOUSE430_2:1451731_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MOE430A:1425496_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MOUSE430A_2:1425496_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MOUSE430_2:1425496_AT ATP-binding cassette, sub-family A (ABC1), member 3 mm
MU11KSUBB:MSA.40645.0_S_AT ATP-binding cassette, sub-family A (ABC1), member 3, mRNA (cDNA clone IMAGE:3596682) mm
MU19KSUBC:TC40078_AT ATP-binding cassette, sub-family A (ABC1), member 3, mRNA (cDNA clone IMAGE:3596682) mm
MU19KSUBC:TC40078_G_AT ATP-binding cassette, sub-family A (ABC1), member 3, mRNA (cDNA clone IMAGE:3596682) mm
RAE230B:1395852_AT ATP-binding cassette, sub-family A (ABC1), member 3 (predicted) rn
RAT230_2:1395852_AT ATP-binding cassette, sub-family A (ABC1), member 3 (predicted) rn
RG-U34B:RC_AA945710_AT ATP-binding cassette, sub-family A (ABC1), member 3 (predicted) 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 AAC69223 Abc transporter family protein 4 [Caenorhabditis elegans] ref|NP_503175.1| ABC Transporter family member (abt-4) [Caenorhabditis elegans] 0.0
blast CAE58173 Hypothetical protein CBG01265 [Caenorhabditis briggsae] 0.0
blast C88925 protein F33E11.4 [imported] - Caenorhabditis elegans 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003439 EMBL-EBI ABC transporter 4.9E-50
Pfam IPR003439 EMBL-EBI ABC transporter 3.9E-42
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503175.1 15 21-43,321-343,364-386,396-418,425-447,502-524,971-993,1073-1092,1099-1121,1157-1179,1209-1231,1235-1257,1270-1292,1302-1324,1371-1390
Y39D8C.1 15 21-43,321-343,364-386,396-418,425-447,502-524,971-993,1073-1092,1099-1121,1157-1179,1209-1231,1235-1257,1270-1292,1302-1324,1371-1390
Sequence
Target Sequence 
>C. ELEGANS:189473_AT
gccgacctcaggtgtggatccaaaggctagacgtattatctggaatattttgaatcgttt
gagagacttgggtactgctcttgtcctcacttctcatagtatggatgaatgtgaagcgtt
gtgcacggaactggcgattatggtttatggaaaattccgatgctatggaagttgtcagca
tatcaagagtagatatggaagtggatacactctgctaatccgtctcaagaaccgaaatga
cgctgaaaagaccaagtcaacgatcaagcaaacattccgcggaagcgtcatcaaggagga
acacgtcctccagctcaactttgacattccacgtgatggagattcgtggtctcgcctctt
cgagaagcttgaaacagtctccacgtcgctcaactgggatgattactcgctgtcgcaaac
cacactggagcaggtgttcatcgaattcagcagggacgccggggtatcttcggattcgga
gtttgatggagccagcagcacagggtcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCGACCTCAGGTGTGGATCCAAAG 300 285 4830 Antisense
AGAGACTTGGGTACTGCTCTTGTCC 199 69 4891 Antisense
CTTGTCCTCACTTCTCATAGTATGG 178 219 4909 Antisense
AAGCGTTGTGCACGGAACTGGCGAT 522 149 4943 Antisense
TGGATACACTCTGCTAATCCGTCTC 556 549 5031 Antisense
CCTCCAGCTCAACTTTGACATTCCA 80 267 5136 Antisense
TGATGGAGATTCGTGGTCTCGCCTC 199 567 5163 Antisense
AGAAGCTTGAAACAGTCTCCACGTC 630 73 5192 Antisense
GATGATTACTCGCTGTCGCAAACCA 99 409 5227 Antisense
CGCCGGGGTATCTTCGGATTCGGAG 225 249 5286 Antisense
TGATGGAGCCAGCAGCACAGGGTCC 239 567 5313 Antisense
Sequence Source Affymetrix Proprietary Database