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[192997_s_at] Vitronectin receptor alpha subunit

Description F54F2.1 /REP_DB=WormBase Gene ID /WP=CE00194 /TR=SW:P34446 /GB=AAK26134.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Vitronectin receptor alpha subunit
Cluster 6grp_highest_10_10 > 20      6grp_high1_10_10 > 14      4grp_high_8_8 > 52      6grp_highest_nonorm > 30      6grp_total > 04      4grp_total > 60      6grp_highest_sub > De      6grp_rule_based > S1      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 736
1 2 3 4 range
A 616.1
(3)
P 		606.9
(2.9)
P 		549.3
(2.3)
P 		29.2
(-3)
A 		587
B 566
(2.6)
P 		604.9
(3)
P 		550.3
(2.4)
P 		62.1
(-3)
P 		543
C 519.8
(0.8)
P 		765.3
(3)
P 		710.2
(2.5)
P 		108.5
(-3)
P 		657
avr 567.3
(2.1) 		659
(3) 		603.3
(2.4) 		66.6
(-3) 		592

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 872
1 2 3 4 5 6 range
A 1158.3
(3)
P 		990.3
(1.8)
P 		619.5
(-0.8)
P 		685.6
(-0.3)
P 		706.3
(-0.2)
P 		299.5
(-3)
P 		859
B 1065.6
(3)
P 		1003.1
(2.5)
P 		769.3
(0.6)
P 		851.2
(1.3)
P 		557.3
(-1.1)
P 		324.8
(-3)
P 		741
C 1130.6
(3)
P 		1044.9
(2.4)
P 		823.5
(0.8)
P 		732.9
(0.2)
P 		590.2
(-0.8)
P 		286.6
(-3)
P 		844
avr 1118.2
(3) 		1012.8
(2.2) 		737.4
(0.2) 		756.6
(0.3) 		617.9
(-0.7) 		303.6
(-3) 		815
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 243
1 2 3 4 range
A 224.3
(3)
P 		131.7
(0.5)
P 		143.6
(0.8)
P 		4.3
(-3)
A 		220
B 180.5
(3)
P 		149.4
(1.9)
P 		127.5
(1.1)
P 		13.2
(-3)
P 		167
C 172.1
(1)
P 		220
(2.3)
P 		247.5
(3)
P 		18.3
(-3)
P 		229
avr 192.3
(3) 		167
(2.2) 		172.9
(2.4) 		11.9
(-3) 		180

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 346
1 2 3 4 5 6 range
A 213.5
(0)
P 		352.2
(3)
P 		134.9
(-1.7)
P 		173.9
(-0.8)
P 		213.1
(0)
P 		72.9
(-3)
P 		279
B 370.8
(3)
P 		333.9
(2.1)
P 		186.8
(-1.4)
P 		225.5
(-0.5)
P 		226.4
(-0.5)
P 		121.1
(-3)
P 		250
C 419.1
(3)
P 		318.8
(1.1)
P 		209.6
(-0.9)
P 		147.4
(-2)
P 		191
(-1.2)
P 		95.9
(-3)
P 		323
avr 334.5
(3) 		335
(3) 		177.1
(-1) 		182.3
(-0.8) 		210.2
(-0.1) 		96.6
(-3) 		238
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192997_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7106
Sequence Type Exemplar sequence
Representative Public ID F54F2.1 NCBI
Target Description F54F2.1 /REP_DB=WormBase Gene ID /WP=CE00194 /TR=SW:P34446 /GB=AAK26134.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Vitronectin receptor alpha subunit
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_066547(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066547 NCBI Caenorhabditis elegans F54F2.1 (F54F2.1) mRNA, complete cds. 11/11 None
SNAP00000044291 ENSEMBL cdna:SNAP chromosome:CEL140:III:8818804:8824880:1 11/11 None
GENEFINDER00000044295 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8818804:8824880:1 11/11 None
F54F2.1 ENSEMBL cdna:known chromosome:CEL140:III:8818804:8825172:1 gene:F54F2.1 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
chrIII:8818799-8824876(+) 100.0 100.0
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:192997_S_AT
taaggctagattctctgatcttcgtgaagctgttaaactttcgaaggaagctggaggagt
tgttgattataagggaccactatcaagagcatctgttgattgtaattcattgagatgtac
acatattgaatgtgatatttatgatcttaaagaagacgagtttgtacttgtggaaatctt
ctctagattatacacaaacacattggttgatgagaaaaatcctggaggagacatttcatc
gttggctcttgctcgtgtcacatctactaaatacaatcttccacataagccaacattgat
aacagcagtatctacaaatatgaatgcaattgcttctgaagaaggaagagatcttccttg
gtggctttatcttttggctattcttattggacttgccattttgattcttcttattttact
gctctggaggtgtggtttcttcaaacgtaatcgtccaccaactgagcatgcaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAAGGCTAGATTCTCTGATCTTCGT 434 637 3117 Antisense
GGGACCACTATCAAGAGCATCTGTT 573 493 3189 Antisense
GTACTTGTGGAAATCTTCTCTAGAT 574 457 3280 Antisense
GAGGAGACATTTCATCGTTGGCTCT 314 403 3341 Antisense
TCTTGCTCGTGTCACATCTACTAAA 150 619 3363 Antisense
ACAATCTTCCACATAAGCCAACATT 695 113 3389 Antisense
GAAGAGATCTTCCTTGGTGGCTTTA 648 337 3461 Antisense
GGTGGCTTTATCTTTTGGCTATTCT 476 499 3476 Antisense
TGATTCTTCTTATTTTACTGCTCTG 138 565 3518 Antisense
TTTCTTCAAACGTAATCGTCCACCA 30 673 3552 Antisense
ATCGTCCACCAACTGAGCATGCAGA 562 35 3566 Antisense
Sequence Source Affymetrix Proprietary Database