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[189434_s_at]

Description F47D12.4 /REP_DB=WormBase Gene ID /WP=CE01948 /CHR=3 /FEA=Sanger Annotation /DEF=locus:hmg-1.2 (ST.LOUIS) SW:Q09390 protein_id:AAA64316.1
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 16      4grp_highest_8_8 > 42      4grp_high_8_8 > 40      6grp_highest_nonorm > 31      6grp_total > 15      4grp_total > 55      6grp_highest_sub > De      6grp_cgc > 23      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 598
1 2 3 4 range
A 1050.9
(3)
P 		767
(-0.4)
P 		728.9
(-0.9)
P 		556.7
(-3)
P 		494
B 1154.3
(3)
P 		640.3
(-2.7)
P 		725.1
(-1.8)
P 		613.7
(-3)
P 		541
C 971.6
(3)
P 		626.8
(-2.8)
P 		774.2
(-0.3)
P 		614.4
(-3)
P 		357
avr 1058.9
(3) 		678
(-1.9) 		742.7
(-1.1) 		594.9
(-3) 		464

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 814
1 2 3 4 5 6 range
A 1156.4
(3)
P 		966.6
(0.2)
P 		775.6
(-2.6)
P 		746.6
(-3)
P 		812.3
(-2)
P 		751.6
(-2.9)
P 		410
B 1145.2
(3)
P 		1109.3
(2.4)
P 		1050.1
(1.3)
P 		824.7
(-2.7)
P 		810.6
(-3)
P 		865.1
(-2)
P 		335
C 1403
(3)
P 		1218.8
(1.6)
P 		807.6
(-1.4)
P 		861.4
(-1)
P 		589.4
(-3)
P 		716.4
(-2.1)
P 		814
avr 1234.9
(3) 		1098.2
(1.4) 		877.8
(-1.3) 		810.9
(-2.1) 		737.4
(-3) 		777.7
(-2.5) 		498
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 301
1 2 3 4 range
A 382.6
(3)
P 		166.5
(-1.3)
P 		190.6
(-0.8)
P 		81.5
(-3)
P 		301
B 368.1
(3)
P 		158.1
(-2.3)
P 		168
(-2.1)
P 		130.8
(-3)
P 		237
C 321.6
(3)
P 		180.2
(-0.9)
P 		269.8
(1.6)
P 		103.6
(-3)
P 		218
avr 357.4
(3) 		168.3
(-1.5) 		209.5
(-0.5) 		105.3
(-3) 		252

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 351
1 2 3 4 5 6 range
A 213.2
(-1.5)
P 		343.8
(3)
P 		168.9
(-3)
P 		189.4
(-2.3)
P 		245.1
(-0.4)
P 		183
(-2.5)
P 		175
B 398.5
(3)
P 		369.2
(2)
P 		255
(-1.8)
P 		218.4
(-3)
P 		329.3
(0.7)
P 		322.6
(0.5)
P 		180
C 520
(3)
P 		371.9
(0.4)
P 		205.6
(-2.4)
P 		173.2
(-3)
P 		190.7
(-2.7)
P 		239.8
(-1.8)
P 		347
avr 377.2
(3) 		361.6
(2.5) 		209.8
(-2.5) 		193.7
(-3) 		255
(-1) 		248.5
(-1.2) 		184
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189434_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7646
Sequence Type Exemplar sequence
Representative Public ID F47D12.4 NCBI
Target Description F47D12.4 /REP_DB=WormBase Gene ID /WP=CE01948 /CHR=3 /FEA=Sanger Annotation /DEF=locus:hmg-1.2 (ST.LOUIS) SW:Q09390 protein_id:AAA64316.1
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_065974(11), NM_001027428(11), NM_001027429(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065974 NCBI Caenorhabditis elegans HMG family member (hmg-1.2) (hmg-1.2) mRNA, complete cds. 11/11 A 
NM_001027428 NCBI Caenorhabditis elegans HMG family member (hmg-1.2) (hmg-1.2) mRNA, complete cds. 11/11 None
NM_001027429 NCBI Caenorhabditis elegans HMG family member (hmg-1.2) (hmg-1.2) mRNA, complete cds. 11/11 None
GENEFINDER00000002711 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:6280546:6281874:1 11/11 None
SNAP00000002702 ENSEMBL cdna:SNAP chromosome:CEL140:III:6280940:6281874:1 11/11 None
F47D12.4a ENSEMBL cdna:known chromosome:CEL140:III:6280341:6282354:1 gene:F47D12.4 11/11 A 
F47D12.4b ENSEMBL cdna:known chromosome:CEL140:III:6280421:6282359:1 gene:F47D12.4 11/11 A 
F47D12.4c ENSEMBL cdna:known chromosome:CEL140:III:6280546:6281874:1 gene:F47D12.4 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:6280938-6281873(+) 100.0 100.0
Public Domain and Genome References
Ensembl F47D12.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK20071 Hmg protein 1.2, isoform a [Caenorhabditis elegans] ref|NP_498375.1| HMG family member (hmg-1.2) [Caenorhabditis elegans] sp|Q09390|HG12_CAEEL High mobility group protein 1.2 gb|AAC78599.1| high mobility group protein 1.2 [Caenorhabditis elegans] 1.0E-132
blast AAK67237 Hmg protein 1.2, isoform b [Caenorhabditis elegans] ref|NP_001022599.1| HMG family member (hmg-1.2) [Caenorhabditis elegans] 1.0E-132
blast AAK67238 Hmg protein 1.2, isoform c [Caenorhabditis elegans] ref|NP_001022600.1| HMG family member (hmg-1.2) [Caenorhabditis elegans] 1.0E-131
blast AAK67237 Hmg protein 1.2, isoform b [Caenorhabditis elegans] ref|NP_001022599.1| HMG family member (hmg-1.2) [Caenorhabditis elegans] 1.0E-130
blast AAK67238 Hmg protein 1.2, isoform c [Caenorhabditis elegans] ref|NP_001022600.1| HMG family member (hmg-1.2) [Caenorhabditis elegans] 1.0E-130
blast AAK20071 Hmg protein 1.2, isoform a [Caenorhabditis elegans] ref|NP_498375.1| HMG family member (hmg-1.2) [Caenorhabditis elegans] sp|Q09390|HG12_CAEEL High mobility group protein 1.2 gb|AAC78599.1| high mobility group protein 1.2 [Caenorhabditis elegans] 1.0E-130
Protein Domains
Database ID Description E-Value
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 2.8E-13
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 9.2E-27
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 2.8E-13
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 9.2E-27
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 1.2E-10
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 9.2E-27
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 1.2E-10
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 9.2E-27
Sequence
Target Sequence 
>C. ELEGANS:189434_S_AT
gggatatgggtaaacctccagtacgaggcaagacatctccatacggattctttgtgaaaa
tgtgctacgaagaacacaagaaaaagtatccgaacgagaatgtccaagtgacagagattt
cgaaaaagtgctcagaaaagtggaagacgatggttgacgatgagaagagacgtttctatg
aactggcacaaaaggacgccgagcgatatcaggcagaggttgccgcttacggaggagaag
atgcgatgaggaagaggaagcgtgccaagaaggatccacatgcaccaaaaagagccctct
cagccttcttcttttactcacaagacaaacgtcctgaaatacaggcaggtcatccagatt
ggaaagtcggacaagttgcacaggagcttggaaaaatgtggaaactagtgccccaggaga
cgaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGGATATGGGTAAACCTCCAGTACG 682 493 32 Antisense
GTACGAGGCAAGACATCTCCATACG 458 459 52 Antisense
GACATCTCCATACGGATTCTTTGTG 59 371 63 Antisense
GAGACGTTTCTATGAACTGGCACAA 558 393 198 Antisense
AGGACGCCGAGCGATATCAGGCAGA 19 57 224 Antisense
GCCAAGAAGGATCCACATGCACCAA 13 279 295 Antisense
CATGCACCAAAAAGAGCCCTCTCAG 263 211 310 Antisense
AGCCTTCTTCTTTTACTCACAAGAC 626 83 333 Antisense
AATACAGGCAGGTCATCCAGATTGG 54 173 369 Antisense
AAGTCGGACAAGTTGCACAGGAGCT 568 157 395 Antisense
GAAACTAGTGCCCCAGGAGACGAAG 422 357 432 Antisense
Sequence Source Affymetrix Proprietary Database