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[173050_at] Vitronectin receptor alpha subunit

Description CEK002H6R_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=D27408 /DEF=C.elegans cDNA clone yk2h6 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 20      6grp_high1_10_10 > 14      4grp_highest_8_8 > 24      4grp_high_8_8 > 51      6grp_highest_nonorm > 51      6grp_total > 04      4grp_total > 60      6grp_highest_sub > De      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 446
1 2 3 4 range
A 490.6
(1.6)
P 		576.8
(3)
P 		460.3
(1.1)
P 		206.4
(-3)
P 		370
B 524
(3)
P 		474.1
(2.2)
P 		485.4
(2.4)
P 		131.2
(-3)
P 		393
C 439.5
(1.2)
P 		517.1
(2.7)
P 		535.2
(3)
P 		212.1
(-3)
P 		323
avr 484.7
(2.3) 		522.7
(3) 		493.6
(2.5) 		183.2
(-3) 		340

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 620
1 2 3 4 5 6 range
A 668.9
(2)
P 		761.1
(3)
P 		441.2
(-0.6)
P 		471.2
(-0.2)
P 		532.7
(0.5)
P 		223.2
(-3)
P 		538
B 801.7
(3)
P 		624.3
(1)
P 		613
(0.8)
P 		594.6
(0.6)
P 		435.8
(-1.2)
P 		275.2
(-3)
P 		527
C 843.3
(3)
P 		611.2
(0.6)
P 		494.6
(-0.6)
P 		701.3
(1.5)
P 		489.3
(-0.6)
P 		259.8
(-3)
P 		584
avr 771.3
(3) 		665.5
(1.8) 		516.3
(0) 		589
(0.9) 		485.9
(-0.3) 		252.7
(-3) 		519
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 159
1 2 3 4 range
A 178.6
(3)
P 		125.2
(0.8)
P 		120.3
(0.6)
P 		30.2
(-3)
P 		148
B 167.1
(3)
P 		117.1
(0.8)
P 		112.5
(0.6)
P 		28
(-3)
P 		139
C 145.5
(1.4)
P 		148.7
(1.5)
P 		186.5
(3)
P 		35.8
(-3)
P 		151
avr 163.7
(3) 		130.3
(1.5) 		139.8
(1.9) 		31.3
(-3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 258
1 2 3 4 5 6 range
A 123.3
(-1.1)
P 		270.7
(3)
P 		96.1
(-1.8)
P 		119.5
(-1.2)
P 		160.8
(-0)
P 		54.3
(-3)
P 		216
B 279
(3)
P 		207.8
(0.6)
P 		148.9
(-1.4)
P 		157.5
(-1.1)
P 		177
(-0.5)
P 		102.6
(-3)
P 		176
C 312.6
(3)
P 		186.5
(-0.4)
P 		125.9
(-2)
P 		141
(-1.6)
P 		158.3
(-1.1)
P 		87
(-3)
P 		226
avr 238.3
(3) 		221.7
(2.4) 		123.6
(-1.4) 		139.3
(-0.8) 		165.4
(0.2) 		81.3
(-3) 		157
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173050_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27318
Sequence Type Exemplar sequence
Representative Public ID CEK002H6R NCBI
Target Description CEK002H6R_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=D27408 /DEF=C.elegans cDNA clone yk2h6 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_066547
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
F54F2.1 ENSEMBL cdna:known chromosome:CEL140:III:8818804:8825172:1 gene:F54F2.1 A 
SNAP00000044291 ENSEMBL cdna:SNAP chromosome:CEL140:III:8818804:8824880:1 None
NM_066547 NCBI Caenorhabditis elegans F54F2.1 (F54F2.1) mRNA, complete cds. A 
GENEFINDER00000044295 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8818804:8824880:1 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
chrIII:8824202-8825143(+) 94.52 95.94
Public Domain and Genome References
Gene Title Vitronectin receptor alpha subunit
Ensembl F54F2.1
Entrez Gene 176240 Entrez gene
SwissProt P34446 EMBL-EBI
WormBase CE00194 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.7930.1.S1_AT similar to Integrin alpha-8 precursor cfa
CANINE_2:CFAAFFX.7943.1.S1_S_AT similar to Integrin alpha-8 precursor cfa
DROSOPHILA_2:1632744_A_AT inflated dm
DROSGENOME1:143200_AT inflated dm
CHICKEN:GGA.1784.1.S1_AT integrin, alpha 8 gga
CHICKEN:GGA.1784.1.S2_AT integrin, alpha 8 gga
HG-U133_PLUS_2:214265_AT integrin, alpha 8 hs
HG-U133A_2:214265_AT integrin, alpha 8 hs
HG-U133A:214265_AT integrin, alpha 8 hs
HG-U133_PLUS_2:239092_AT integrin, alpha 8 hs
HG-U133B:239092_AT integrin, alpha 8 hs
HU35KSUBA:L36531_AT integrin, alpha 8 hs
HUGENEFL:L36531_AT integrin, alpha 8 hs
U133_X3P:HS.91296.0.A1_3P_AT integrin, alpha 8 hs
U133_X3P:HS.171025.0.A1_3P_AT integrin, alpha 8 hs
U133_X3P:HS.168014.0.A1_3P_AT integrin, alpha 8 hs
HG-U133_PLUS_2:242071_X_AT integrin, alpha 8 hs
HG-U133B:242071_X_AT integrin, alpha 8 hs
HG-U95AV2:41005_AT integrin, alpha 8 hs
HG-U95C:62298_AT integrin, alpha 8 hs
HG-U95D:92019_R_AT integrin, alpha 8 hs
HU35KSUBD:RC_AA599597_AT Integrin, alpha 8 hs
MG-U74AV2:100314_F_AT integrin alpha 8 mm
MOE430A:1427489_AT integrin alpha 8 mm
MOUSE430A_2:1427489_AT integrin alpha 8 mm
MOUSE430_2:1427489_AT integrin alpha 8 mm
MG-U74AV2:100313_AT integrin alpha 8 mm
MG-U74CV2:166680_AT integrin alpha 8 mm
MOE430B:1454966_AT integrin alpha 8 mm
MOUSE430_2:1454966_AT integrin alpha 8 mm
MG-U74CV2:129876_AT Integrin alpha 8 (Itga8), mRNA mm
RG-U34A:RC_AI639291_AT similar to integrin alpha 8 rn
RAE230A:1385354_AT similar to integrin alpha 8 rn
RAT230_2:1385354_AT similar to integrin alpha 8 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7155 cell adhesion inferred from electronic annotation QuickGO AmiGO
7160 cell-matrix adhesion inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
8305 integrin complex inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK26134 Hypothetical protein F54F2.1 [Caenorhabditis elegans] ref|NP_498948.1| F54F2.1 [Caenorhabditis elegans] sp|P34446|PAT2_CAEEL Integrin alpha pat-2 precursor 0.0
blast CAE62730 Hypothetical protein CBG06891 [Caenorhabditis briggsae] 0.0
blast AAO85804 integrin alpha 2 [Pseudoplusia includens] 1.0E-118
Protein Domains
Database ID Description E-Value
Pfam IPR000413 EMBL-EBI Integrins alpha chain 1.0E-7
Pfam IPR000413 EMBL-EBI Integrins alpha chain 3.3E-7
Pfam IPR000413 EMBL-EBI Integrins alpha chain 2.0E-5
Pfam IPR000413 EMBL-EBI Integrins alpha chain 9.3E-8
Pfam IPR000413 EMBL-EBI Integrins alpha chain 2.1E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498948.1 1 1155-1177
F54F2.1 1 1155-1177
SNAP00000044291 1 1155-1177
GENEFINDER00000044295 1 1155-1177
Sequence
Target Sequence 
>C. ELEGANS:173050_AT
cctggtgcttatcttttgctaatcttattggacttgccantttgattccttcttatttta
cttgctctggaggtgtggtttcctccaaacgtaatcgtcccacccaactgagcatgcaag
aactccgtgccgacccgtcaacccaaatgctcaatacgctgatagtcaatcccgttatac
atcacaagatcagtacaatcagggacgtcacggacaaatgctataatattttccattttt
tgttccttattctttactattcacatctgcgggtgtctttttaaaattatcattttggtc
ccaatttagtcctcttgtcgtgccttgccccccaatcttactttcatgttcgatcgtttt
tcggaatctccgctcaatttggtgctttatatgttcatattatgtttctttgttttccaa
ttaattaccaatacattgacatgtttctagtcgatatttttga

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCTGGTGCTTATCTTTTGCTAATCT 649 261 13 Antisense
CTTTTGCTAATCTTATTGGACTTGC 85 223 25 Antisense
TCCCACCCAACTGAGCATGCAAGAA 394 597 110 Antisense
GTTCCTTATTCTTTACTATTCACAT 385 441 254 Antisense
TATTCACATCTGCGGGTGTCTTTTT 626 659 270 Antisense
CATTTTGGTCCCAATTTAGTCCTCT 290 215 303 Antisense
CCCCCAATCTTACTTTCATGTTCGA 364 261 341 Antisense
TTCGATCGTTTTTCGGAATCTCCGC 28 697 361 Antisense
AATCTCCGCTCAATTTGGTGCTTTA 69 171 377 Antisense
CATATTATGTTTCTTTGTTTTCCAA 115 215 408 Antisense
ACATGTTTCTAGTCGATATTTTTGA 122 107 451 Antisense
Sequence Source Affymetrix Proprietary Database