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[193484_s_at] single-strand recognition protein

Description C32F10.5 /REP_DB=WormBase Gene ID /WP=CE08542 /GEN=hmg-3 /TR=O01683 /GB=AAC24268.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=single-strand recognition protein
Cluster 6grp_total > 97      4grp_total > 24      6grp_cgc > 68      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 213
1 2 3 4 range
A 51.9
(-3)
A 		75.4
(-2.1)
A 		124.1
(-0.1)
A 		200.8
(3)
A 		149
B 39.6
(-2)
A 		12
(-3)
A 		154.8
(2.4)
A 		170.2
(3)
A 		158
C 18
(-3)
A 		108.7
(-0.4)
A 		138.4
(0.5)
A 		224.5
(3)
A 		207
avr 36.5
(-3) 		65.4
(-1.9) 		139.1
(0.8) 		198.5
(3) 		162

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 806
1 2 3 4 5 6 range
A 10.9
(-3)
A 		22.5
(-2.9)
A 		150.2
(-1.7)
A 		237.3
(-1)
P 		430.3
(0.8)
P 		678.8
(3)
P 		668
B 39.7
(-3)
A 		53.9
(-2.9)
A 		180.8
(-1.9)
A 		220.3
(-1.6)
M 		566.9
(1.2)
P 		792.2
(3)
P 		753
C 31.4
(-3)
A 		41.8
(-2.9)
A 		138
(-2.2)
A 		300.5
(-0.9)
P 		405.5
(-0.1)
P 		816.4
(3)
P 		785
avr 27.3
(-3) 		39.4
(-2.9) 		156.3
(-1.9) 		252.7
(-1.2) 		467.6
(0.6) 		762.5
(3) 		735
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 45
1 2 3 4 range
A 18.9
(-2.1)
A 		16.4
(-3)
A 		32.4
(3)
A 		29.4
(1.9)
A 		16
B 12.6
(-1.3)
A 		3
(-3)
A 		35.9
(2.9)
A 		36.3
(3)
A 		33
C 6
(-3)
A 		31.3
(0.6)
A 		48.2
(3)
A 		37.9
(1.5)
A 		42
avr 12.5
(-3) 		16.9
(-2) 		38.8
(3) 		34.5
(2) 		26

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 293
1 2 3 4 5 6 range
A 2
(-3)
A 		8
(-2.8)
A 		32.7
(-1.9)
A 		60.2
(-0.9)
P 		129.8
(1.7)
P 		165.3
(3)
P 		163
B 13.8
(-3)
A 		17.9
(-2.9)
A 		43.9
(-2.4)
A 		58.4
(-2)
M 		230.3
(1.6)
P 		295.4
(3)
P 		282
C 11.6
(-3)
A 		12.8
(-3)
A 		35.1
(-2.5)
A 		60.4
(-1.9)
P 		131.2
(-0.3)
P 		273.3
(3)
P 		262
avr 9.1
(-3) 		12.9
(-2.9) 		37.2
(-2.3) 		59.7
(-1.7) 		163.8
(0.9) 		244.7
(3) 		236
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193484_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2191
Sequence Type Exemplar sequence
Representative Public ID C32F10.5 NCBI
Target Description C32F10.5 /REP_DB=WormBase Gene ID /WP=CE08542 /GEN=hmg-3 /TR=O01683 /GB=AAC24268.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=single-strand recognition protein
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_059287(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059287 NCBI Caenorhabditis elegans HMG family member (hmg-3) (hmg-3) mRNA, complete cds. 11/11 None
SNAP00000021236 ENSEMBL cdna:SNAP chromosome:CEL140:I:5823895:5826261:-1 11/11 None
GENEFINDER00000021244 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5823895:5826261:-1 11/11 None
C32F10.5 ENSEMBL cdna:known chromosome:CEL140:I:5823809:5826261:-1 gene:C32F10.5 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
chrI:5823894-5826261(-) 95.75 100.0
Public Domain and Genome References
Gene Title single-strand recognition protein
Gene Symbol hmg-3
Ensembl C32F10.5
Entrez Gene 172250 Entrez gene
SwissProt O01683 EMBL-EBI
WormBase CE08542 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
785 chromatin inferred from electronic annotation QuickGO AmiGO
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC24268 Hmg protein 3 [Caenorhabditis elegans] ref|NP_491688.1| HMG family member (hmg-3) [Caenorhabditis elegans] 0.0
blast AAA19061 Hmg protein 4 [Caenorhabditis elegans] ref|NP_498633.1| HMG family member (hmg-4) [Caenorhabditis elegans] sp|P41848|SSRP_CAEEL Probable structure-specific recognition protein 1 (SSRP1) (Recombination signal sequence recognition protein) 0.0
blast CAE64433 Hypothetical protein CBG09136 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000969 EMBL-EBI Structure-specific recognition protein 1.0E-126
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 1.9E-21
Sequence
Target Sequence 
>C. ELEGANS:193484_S_AT
ccaaatgagccgaaacgagcaaccactgcatatatcatctggttcaatgccaatcgtaat
tcaatgaaagaagatggggatacactcggagatgttgctaaaaaagccggagcaaagtgg
aagtccatgagtgcggatgataaaaaggaatggaacgataaggctgcacaggacaaggca
agatacgaagcggaaatgaaagaatacaagaagaatggtggaggagtagagaaagcatct
ggaccatccacgaagaaaagctccgatcaatctccgggtaaacagttcaagtctaaggag
catatcagtgatacggatgattccgatgacgatgagccgctaaaggcga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAAATGAGCCGAAACGAGCAACCA 38 275 1684 Antisense
GAGCAACCACTGCATATATCATCTG 203 391 1700 Antisense
ATCATCTGGTTCAATGCCAATCGTA 460 29 1717 Antisense
GGGGATACACTCGGAGATGTTGCTA 698 497 1759 Antisense
GTGGAAGTCCATGAGTGCGGATGAT 548 491 1800 Antisense
GAATGGAACGATAAGGCTGCACAGG 209 333 1831 Antisense
AGAGAAAGCATCTGGACCATCCACG 600 69 1911 Antisense
GACCATCCACGAAGAAAAGCTCCGA 647 383 1925 Antisense
AAAGCTCCGATCAATCTCCGGGTAA 499 123 1940 Antisense
CAATCTCCGGGTAAACAGTTCAAGT 286 155 1951 Antisense
GATGACGATGAGCCGCTAAAGGCGA 312 409 2008 Antisense
Sequence Source Affymetrix Proprietary Database