[Home] | [Total List]

[173427_at]

Description g3293317-REP_DB=GenBank Identifier /5_PRIME_EXT_ID=g3293317 /5_PRIME_EXT_DB=GenBank Identifier /CHR=4 /FEA=Genomic Cluster /GEN=soc-2 /DEF=leucine-rich repeat protein SOC-2
Cluster 6grp_highest_10_10 > 70      6grp_high1_10_10 > 05      4grp_highest_8_8 > 24      4grp_high_8_8 > 51      6grp_highest_nonorm > 21      6grp_total > 04      4grp_total > 60      6grp_highest_sub > De      6grp_cgc > 22      6grp_high1_sub > De      6grp_cgc_sub > De      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1685
1 2 3 4 range
A 1819.2
(3)
P 		1693.4
(2.5)
P 		1715
(2.6)
P 		356.9
(-3)
P 		1462
B 1942.7
(2.6)
P 		1924.9
(2.5)
P 		2041.4
(3)
P 		623.2
(-3)
P 		1418
C 1944.3
(2.6)
P 		2041.9
(3)
P 		1822.8
(2.2)
P 		402.5
(-3)
P 		1639
avr 1902.1
(3) 		1886.7
(2.9) 		1859.7
(2.8) 		460.9
(-3) 		1441

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1428
1 2 3 4 5 6 range
A 1817
(3)
P 		1390.1
(0.6)
P 		1024.3
(-1.4)
P 		957.9
(-1.8)
P 		1230.4
(-0.3)
P 		747.8
(-3)
P 		1069
B 1778.6
(3)
P 		1472.3
(1.1)
P 		1019.7
(-1.6)
P 		1154.1
(-0.8)
P 		984.9
(-1.8)
P 		793.5
(-3)
P 		985
C 1996.9
(3)
P 		1261.1
(-0.1)
P 		1137.7
(-0.6)
P 		1213.8
(-0.3)
P 		1038.9
(-1)
P 		568.5
(-3)
P 		1428
avr 1864.2
(3) 		1374.5
(0.5) 		1060.6
(-1.2) 		1108.6
(-0.9) 		1084.7
(-1) 		703.3
(-3) 		1161
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 610
1 2 3 4 range
A 662.4
(3)
P 		367.6
(0.1)
P 		448.3
(0.9)
P 		52.2
(-3)
P 		610
B 619.5
(3)
P 		475.4
(1.2)
P 		473
(1.2)
P 		132.8
(-3)
P 		487
C 643.6
(3)
P 		587
(2.4)
P 		635.3
(2.9)
P 		67.9
(-3)
P 		576
avr 641.8
(3) 		476.7
(1.2) 		518.9
(1.7) 		84.3
(-3) 		558

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 558
1 2 3 4 5 6 range
A 334.9
(-0.1)
P 		494.4
(3)
P 		223.1
(-2.2)
P 		242.9
(-1.8)
P 		371.3
(0.6)
P 		182.1
(-3)
P 		312
B 618.9
(3)
P 		490.1
(0.9)
P 		247.6
(-3)
P 		305.7
(-2.1)
P 		400.2
(-0.5)
P 		295.9
(-2.2)
P 		371
C 740.2
(3)
P 		384.8
(-0.9)
P 		289.6
(-1.9)
P 		244.1
(-2.4)
P 		336.2
(-1.4)
P 		190.3
(-3)
P 		550
avr 564.7
(3) 		456.4
(1.1) 		253.4
(-2.5) 		264.2
(-2.3) 		369.2
(-0.4) 		222.8
(-3) 		342
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173427_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24931
Sequence Type Exemplar sequence
Representative Public ID 3293317 NCBI
Target Description g3293317-REP_DB=GenBank Identifier /5_PRIME_EXT_ID=g3293317 /5_PRIME_EXT_DB=GenBank Identifier /CHR=4 /FEA=Genomic Cluster /GEN=soc-2 /DEF=leucine-rich repeat protein SOC-2
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_171332(11), NM_001026088(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171332 NCBI Caenorhabditis elegans Suppressor Of Clr family member (soc-2) (soc-2) mRNA, complete cds. 11/11 A 
NM_001026088 NCBI Caenorhabditis elegans Suppressor Of Clr family member (soc-2) (soc-2) mRNA, complete cds. 11/11 None
AC7.2b.1 ENSEMBL cdna:known chromosome:CEL140:IV:5126996:5145800:-1 gene:AC7.2 11/11 A 
AC7.2a.1 ENSEMBL cdna:known chromosome:CEL140:IV:5127035:5133847:-1 gene:AC7.2 11/11 None
AC7.2b.2 ENSEMBL cdna:known chromosome:CEL140:IV:5127068:5145800:-1 gene:AC7.2 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
chrIV:5127040-5133856(-) 98.97 100.0
Public Domain and Genome References
Ensembl AC7.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAM81129 Suppressor of clr protein 2, isoform b [Caenorhabditis elegans] ref|NP_741391.2| Suppressor Of Clr family member (soc-2) [Caenorhabditis elegans] 0.0
blast AAB03417 Suppressor of clr protein 2, isoform a [Caenorhabditis elegans] ref|NP_001021259.1| Suppressor Of Clr family member (soc-2) [Caenorhabditis elegans] gb|AAC39129.1| Ras-binding protein SUR-8 [Caenorhabditis elegans] gb|AAC25697.1| leucine-rich repeat protein SOC-2 [Caenorhabditis elegans] 0.0
blast CAE72750 Hypothetical protein CBG19995 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.027
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0048
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0054
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.01
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.01
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0012
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.065
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.29
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.27
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.081
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0046
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 6.6E-4
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0069
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.093
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0064
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.15
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.027
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0048
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0054
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.01
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.01
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0012
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.065
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.29
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.27
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.081
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0046
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 6.6E-4
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0069
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.093
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0064
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.15
Sequence
Target Sequence 
>C. ELEGANS:173427_AT
aattctcaataattcccccaatattctacttcaattcaaaaaaccatgtttcttgtcttc
tacgggttgcaaaacttgttttcgctccaaaatgttttttttaatgttttatttttttga
aactgaaaagtcactttttcttctcaaaatatcatattaatatggtacttttccaattca
attgtgtcttcccgattttttctctcaaaaaaggttttgtttattaattattttcaaatt
gtgaattccaaaaactttctctcgtccagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATTCTCAATAATTCCCCCAATATT 602 175 1771 Antisense
ATTCCCCCAATATTCTACTTCAATT 436 9 1782 Antisense
CCCCCAATATTCTACTTCAATTCAA 363 261 1785 Antisense
TTCTACTTCAATTCAAAAAACCATG 283 687 1794 Antisense
AAAACCATGTTTCTTGTCTTCTACG 240 129 1810 Antisense
ACCATGTTTCTTGTCTTCTACGGGT 469 85 1813 Antisense
TTCTTGTCTTCTACGGGTTGCAAAA 174 689 1820 Antisense
GGTTGCAAAACTTGTTTTCGCTCCA 89 509 1835 Antisense
CAAAACTTGTTTTCGCTCCAAAATG 651 189 1840 Antisense
AATATGGTACTTTTCCAATTCAATT 475 173 1929 Antisense
TTCCAAAAACTTTCTCTCGTCCAGT 649 695 2016 Antisense
Sequence Source GenBank