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[174707_s_at] alpha-catenin

Description CEK036D4R_rc /REP_DB=TREMBL Accession /GB=D33803 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk36d4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 75      6grp_high1_10_10 > 57      4grp_highest_8_8 > 42      4grp_high_8_8 > 49      6grp_highest_nonorm > 84      6grp_total > 57      4grp_total > 62      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 244
1 2 3 4 range
A 510
(3)
P 		358.9
(-1.2)
P 		346.4
(-1.5)
P 		293.3
(-3)
P 		217
B 483.4
(3)
P 		339.4
(-1)
P 		408.4
(0.9)
P 		266.3
(-3)
P 		217
C 488.1
(3)
P 		357.2
(-0.7)
P 		425.9
(1.2)
P 		276.7
(-3)
P 		211
avr 493.8
(3) 		351.8
(-1) 		393.6
(0.2) 		278.8
(-3) 		215

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 416
1 2 3 4 5 6 range
A 509.4
(-1.4)
P 		576.8
(0.4)
P 		447.2
(-3)
P 		518.1
(-1.1)
P 		450.5
(-2.9)
P 		676
(3)
P 		229
B 641.1
(0.3)
P 		470.9
(-2.1)
P 		458.2
(-2.3)
P 		528.7
(-1.3)
P 		410.1
(-3)
P 		825.7
(3)
P 		416
C 717.9
(1.9)
P 		600.9
(-0.5)
P 		498.9
(-2.5)
P 		511.6
(-2.3)
P 		476.8
(-3)
P 		769.3
(3)
P 		293
avr 622.8
(0.4) 		549.5
(-1) 		468.1
(-2.6) 		519.5
(-1.6) 		445.8
(-3) 		757
(3) 		311
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 143
1 2 3 4 range
A 185.7
(3)
P 		77.9
(-1.5)
P 		90.6
(-1)
P 		42.9
(-3)
P 		143
B 154.1
(3)
P 		83.8
(-1.3)
P 		94.6
(-0.7)
P 		56.7
(-3)
P 		97
C 161.6
(3)
P 		102.7
(-0.1)
P 		148.4
(2.3)
P 		46.7
(-3)
P 		115
avr 167.1
(3) 		88.1
(-1) 		111.2
(0.2) 		48.8
(-3) 		118

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 214
1 2 3 4 5 6 range
A 93.9
(-3)
P 		205.2
(3)
P 		97.4
(-2.8)
P 		131.4
(-1)
P 		135.9
(-0.7)
P 		164.6
(0.8)
P 		111
B 223.1
(0.4)
P 		156.8
(-1.6)
P 		111.3
(-3)
P 		140
(-2.1)
P 		166.6
(-1.3)
P 		307.9
(3)
P 		197
C 266.1
(3)
P 		183.4
(-0)
P 		127
(-2.1)
P 		102.9
(-3)
P 		154.3
(-1.1)
P 		257.5
(2.7)
P 		163
avr 194.4
(0.8) 		181.8
(0.2) 		111.9
(-3) 		124.8
(-2.4) 		152.3
(-1.2) 		243.3
(3) 		131
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174707_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21890
Sequence Type Exemplar sequence
Representative Public ID CEK036D4R NCBI
Target Description CEK036D4R_rc /REP_DB=TREMBL Accession /GB=D33803 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk36d4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_073584(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073584 NCBI Caenorhabditis elegans R13H4.4 (alpha-catenin) mRNA, complete cds. 11/11 A 
SNAP00000036683 ENSEMBL cdna:SNAP chromosome:CEL140:V:11848466:11854358:1 11/11 None
GENEFINDER00000036691 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11848466:11854358:1 11/11 None
R13H4.4 ENSEMBL cdna:known chromosome:CEL140:V:11848465:11854752:1 gene:R13H4.4 11/11 A 
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:11851952-11852332(+) 99.21 100.0
Public Domain and Genome References
Gene Title alpha-catenin
Gene Symbol hmp-1
Ensembl R13H4.4
Entrez Gene 179624 Entrez gene
SwissProt P90947 EMBL-EBI
WormBase CE25089 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1598149_AT similar to catenin, alpha 2 cfa
CANINE_2:CFA.9512.1.A1_AT similar to catenin, alpha 2 cfa
CANINE_2:CFAAFFX.12905.1.S1_S_AT similar to catenin, alpha 2 cfa
CANINE_2:CFAAFFX.12908.1.S1_AT similar to catenin, alpha 2 cfa
CANINE_2:CFAAFFX.12938.1.S1_AT similar to catenin, alpha 2 cfa
DROSOPHILA_2:1632724_AT Catenin dm
DROSGENOME1:154527_AT Catenin dm
CHICKEN:GGA.2375.1.S1_AT catenin (cadherin-associated protein), alpha 2 gga
CHICKEN:GGA.2375.1.S2_AT catenin (cadherin-associated protein), alpha 2 gga
CHICKEN:GGAAFFX.24818.1.S1_AT catenin (cadherin-associated protein), alpha 2 gga
HG-U95AV2:208_AT catenin (cadherin-associated protein), alpha 2 hs
HC-G110:208_AT catenin (cadherin-associated protein), alpha 2 hs
HG-U95AV2:31841_AT catenin (cadherin-associated protein), alpha 2 hs
HU35KSUBD:RC_R37305_F_AT catenin (cadherin-associated protein), alpha 2 hs
HU35KSUBD:RC_H16079_F_AT catenin (cadherin-associated protein), alpha 2 hs
HUGENEFL:M94151_AT catenin (cadherin-associated protein), alpha 2 hs
HG-U133A:205373_AT catenin (cadherin-associated protein), alpha 2 hs
HG-U133_PLUS_2:205373_AT catenin (cadherin-associated protein), alpha 2 hs
HG-FOCUS:205373_AT catenin (cadherin-associated protein), alpha 2 hs
HG-U133A_2:205373_AT catenin (cadherin-associated protein), alpha 2 hs
U133_X3P:G7656998_3P_AT catenin (cadherin-associated protein), alpha 2 hs
HG-U95C:54645_AT catenin (cadherin-associated protein), alpha 2 hs
HG-U95B:42611_AT Catenin (cadherin-associated protein), alpha 2 hs
HG-U95C:66711_AT Catenin (cadherin-associated protein), alpha 2 hs
HU35KSUBA:AA082824_AT Catenin (cadherin-associated protein), alpha 2 hs
HU35KSUBD:RC_H10781_AT Catenin (cadherin-associated protein), alpha 2 hs
MOUSE430_2:1448895_A_AT catenin (cadherin associated protein), alpha 2 mm
MOE430A:1448895_A_AT catenin (cadherin associated protein), alpha 2 mm
MOUSE430A_2:1448895_A_AT catenin (cadherin associated protein), alpha 2 mm
MU11KSUBA:D25282_S_AT catenin (cadherin associated protein), alpha 2 mm
MG-U74AV2:92228_AT catenin (cadherin associated protein), alpha 2 mm
MG-U74AV2:92227_S_AT catenin (cadherin associated protein), alpha 2 mm
MG-U74AV2:161318_F_AT catenin (cadherin associated protein), alpha 2 mm
MU19KSUBB:TC25947_S_AT Catenin (cadherin associated protein), alpha 2 (Ctnna2), transcript variant 1, mRNA mm
RG-U34B:RC_AI058441_AT Catenin alpha 2 (predicted) rn
RG-U34C:RC_AI071716_AT Catenin alpha 2 (predicted) rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5913 cell-cell adherens junction inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
51015 actin filament binding traceable author statement QuickGO AmiGO
8013 beta-catenin binding inferred from physical interaction QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB61019 Hypothetical protein R13H4.4 [Caenorhabditis elegans] ref|NP_505985.1| R13H4.4 [Caenorhabditis elegans] gb|AAB94551.1| HMP-1 [Caenorhabditis elegans] 0.0
blast T24221 hypothetical protein R13H4.4 - Caenorhabditis elegans 0.0
blast CAE75281 Hypothetical protein CBG23248 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006077 EMBL-EBI Vinculin/alpha-catenin 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:174707_S_AT
ggaaatgagcttgtcgtatctgcacttgactctgcaatgtctcttattcaaacggctcga
aatcttttaactgctgttgtacagactgttaaagctgcatacattgccagtaccaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAAATGAGCTTGTCGTATCTGCAC 250 527 23 Antisense
TGAGCTTGTCGTATCTGCACTTGAC 484 569 28 Antisense
TTGTCGTATCTGCACTTGACTCTGC 326 705 33 Antisense
GCACTTGACTCTGCAATGTCTCTTA 598 315 44 Antisense
GACTCTGCAATGTCTCTTATTCAAA 582 373 50 Antisense
AATGTCTCTTATTCAAACGGCTCGA 219 163 58 Antisense
CTCTTATTCAAACGGCTCGAAATCT 416 223 63 Antisense
GAAATCTTTTAACTGCTGTTGTACA 293 363 81 Antisense
TAACTGCTGTTGTACAGACTGTTAA 356 639 90 Antisense
GACTGTTAAAGCTGCATACATTGCC 16 377 106 Antisense
AGCTGCATACATTGCCAGTACCAAG 468 81 115 Antisense
Sequence Source Affymetrix Proprietary Database