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[188651_s_at]

Description T20B12.8 /REP_DB=WormBase Gene ID /WP=CE01414 /GEN=hmg-4 /TR=SW:P41848 /GB=AAA19061.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 74      6grp_high1_10_10 > 56      4grp_highest_8_8 > 42      4grp_high_8_8 > 40      6grp_highest_nonorm > 86      6grp_total > 57      4grp_total > 54      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 550
1 2 3 4 range
A 1102.5
(3)
P 		782.1
(-1.4)
P 		730.6
(-2.1)
P 		668.3
(-3)
P 		434
B 1072.4
(3)
P 		770.7
(-2)
P 		809.7
(-1.4)
P 		711.2
(-3)
P 		361
C 1179.2
(3)
P 		823.8
(-0.9)
P 		847
(-0.6)
P 		629.1
(-3)
P 		550
avr 1118
(3) 		792.2
(-1.4) 		795.8
(-1.3) 		669.5
(-3) 		449

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 862
1 2 3 4 5 6 range
A 927.7
(0.6)
P 		885.4
(-0.3)
P 		1036.9
(3)
P 		761.2
(-3)
P 		789.9
(-2.4)
P 		918.5
(0.4)
P 		276
B 1148.3
(0.3)
P 		877.8
(-2)
P 		767.1
(-3)
P 		817.4
(-2.6)
P 		850.2
(-2.3)
P 		1459
(3)
P 		692
C 991.6
(0.2)
P 		1050.4
(0.6)
P 		911.3
(-0.5)
P 		706.5
(-2.1)
P 		596.8
(-3)
P 		1347.7
(3)
P 		751
avr 1022.5
(0.3) 		937.9
(-0.7) 		905.1
(-1.1) 		761.7
(-2.8) 		745.6
(-3) 		1241.7
(3) 		496
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 304
1 2 3 4 range
A 401.4
(3)
P 		169.8
(-1.6)
P 		191
(-1.2)
P 		97.8
(-3)
P 		304
B 342
(3)
P 		190.3
(-1.8)
P 		187.6
(-1.9)
P 		151.6
(-3)
P 		190
C 390.4
(3)
P 		236.8
(-0.2)
P 		295.2
(1)
P 		106.1
(-3)
P 		284
avr 377.9
(3) 		199
(-1.1) 		224.6
(-0.5) 		118.5
(-3) 		259

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 402
1 2 3 4 5 6 range
A 171
(-3)
P 		314.9
(3)
P 		225.8
(-0.7)
P 		193
(-2.1)
P 		238.4
(-0.2)
P 		223.6
(-0.8)
P 		144
B 399.6
(0.6)
P 		292.2
(-1.2)
P 		186.3
(-3)
P 		216.5
(-2.5)
P 		345.4
(-0.3)
P 		544.1
(3)
P 		358
C 367.5
(1.4)
P 		320.5
(0.5)
P 		231.9
(-1.3)
P 		142.1
(-3)
P 		193.1
(-2)
P 		451.2
(3)
P 		309
avr 312.7
(0.5) 		309.2
(0.4) 		214.7
(-2.2) 		183.9
(-3) 		259
(-1) 		406.3
(3) 		222
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188651_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7178
Sequence Type Exemplar sequence
Representative Public ID T20B12.8 NCBI
Target Description T20B12.8 /REP_DB=WormBase Gene ID /WP=CE01414 /GEN=hmg-4 /TR=SW:P41848 /GB=AAA19061.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=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_066232(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066232 NCBI Caenorhabditis elegans HMG family member (hmg-4) (hmg-4) mRNA, complete cds. 11/11 None
SNAP00000022558 ENSEMBL cdna:SNAP chromosome:CEL140:III:7379201:7381515:-1 11/11 None
GENEFINDER00000022570 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7379201:7381515:-1 11/11 None
T20B12.8 ENSEMBL cdna:known chromosome:CEL140:III:7379074:7381516:-1 gene:T20B12.8 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:7379198-7381513(-) 94.6 100.0
Public Domain and Genome References
Gene Title
Gene Symbol hmg-4
Ensembl T20B12.8
Entrez Gene 176052 Entrez gene
SwissProt P41848 EMBL-EBI
WormBase CE01414 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:16147_S_AT structure-specific recognition protein 1 / high mobility group protein / HMG protein at
ATH1-121501:256590_AT structure-specific recognition protein 1 / high mobility group protein / HMG protein at
CANINE:1584683_X_AT similar to structure specific recognition protein 1 cfa
CANINE:1588143_S_AT similar to structure specific recognition protein 1 cfa
CANINE:1586120_X_AT similar to structure specific recognition protein 1 cfa
CANINE_2:CFA.635.1.A1_S_AT similar to structure specific recognition protein 1 cfa
CANINE_2:CFA.635.1.A2_AT similar to structure specific recognition protein 1 cfa
DROSOPHILA_2:1624815_AT Structure specific recognition protein dm
DROSGENOME1:141661_AT Structure specific recognition protein dm
HG-U133_PLUS_2:200957_S_AT structure specific recognition protein 1 hs
HG-U133A:200957_S_AT structure specific recognition protein 1 hs
HG-FOCUS:200957_S_AT structure specific recognition protein 1 hs
HG-U133A_2:200957_S_AT structure specific recognition protein 1 hs
HG-U133_PLUS_2:200956_S_AT structure specific recognition protein 1 hs
HG-U133A_2:200956_S_AT structure specific recognition protein 1 hs
HG-U133A:200956_S_AT structure specific recognition protein 1 hs
HUGENEFL:M86737_AT structure specific recognition protein 1 hs
U133_X3P:G4507240_3P_A_AT structure specific recognition protein 1 hs
U133_X3P:HS.79162.0.S1_3P_A_AT structure specific recognition protein 1 hs
HG-U95AV2:37739_AT structure specific recognition protein 1 hs
MU11KSUBB:W30290_S_AT structure specific recognition protein 1 mm
MG-U74AV2:95069_AT structure specific recognition protein 1 mm
MOE430A:1426789_S_AT structure specific recognition protein 1 mm
MOUSE430A_2:1426789_S_AT structure specific recognition protein 1 mm
MOUSE430_2:1426789_S_AT structure specific recognition protein 1 mm
MOE430A:1426788_A_AT structure specific recognition protein 1 mm
MOUSE430A_2:1426788_A_AT structure specific recognition protein 1 mm
MOUSE430_2:1426788_A_AT structure specific recognition protein 1 mm
MOE430A:1426790_AT structure specific recognition protein 1 mm
MOUSE430A_2:1426790_AT structure specific recognition protein 1 mm
MOUSE430_2:1426790_AT structure specific recognition protein 1 mm
MOE430B:1458396_AT Structure specific recognition protein 1 (Ssrp1), mRNA mm
MOUSE430_2:1458396_AT Structure specific recognition protein 1 (Ssrp1), mRNA mm
MU19KSUBA:TC20081_AT Structure specific recognition protein 1 (Ssrp1), mRNA mm
RT-U34:L08814_AT structure specific recognition protein 1 rn
RG-U34A:L08814_AT structure specific recognition protein 1 rn
RAE230A:1388129_AT structure specific recognition protein 1 rn
RAT230_2:1388129_AT structure specific recognition protein 1 rn
YEAST_2:1779542_AT Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure Sc
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 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 AAC24268 Hmg protein 3 [Caenorhabditis elegans] ref|NP_491688.1| HMG family member (hmg-3) [Caenorhabditis elegans] 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 2.8E-20
Sequence
Target Sequence 
>C. ELEGANS:188651_S_AT
agtggaactggagagtctgagccggattctgagcaagatgttccgtcgaagcgaagaaag
ggtgaacctaaagagaagagggaaaagaaggagaaaagagaaaagaaggaaggcaagaaa
ggaaagaaagacaaagatccaaacgctccgaaacgtgctacaagtgcctacatgcaatgg
ttccttgctagtcgaaatgaactgaaggaggatggtgattctgttgctgatgtggccaag
aaaggtggagccaaatggaaaacgatgagctcggatgataaaaagaaatgggaggaaaaa
gcagaagaagataagtctcgatacgagaaagaaatgaaggaatacagaaagaatggacca
ccatcttcctcgtcaaaaccatcttcatcaaaaacatcaaagaaaagttctggaccatct
tcatccaaggccatttcgaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGTGGAACTGGAGAGTCTGAGCCGG 594 57 1531 Antisense
GAGTCTGAGCCGGATTCTGAGCAAG 131 401 1543 Antisense
TCTGAGCAAGATGTTCCGTCGAAGC 517 607 1558 Antisense
GACAAAGATCCAAACGCTCCGAAAC 26 367 1660 Antisense
GCTCCGAAACGTGCTACAAGTGCCT 427 295 1675 Antisense
CAAGTGCCTACATGCAATGGTTCCT 107 185 1691 Antisense
CAATGGTTCCTTGCTAGTCGAAATG 650 181 1705 Antisense
GGTGATTCTGTTGCTGATGTGGCCA 17 501 1744 Antisense
TCCTCGTCAAAACCATCTTCATCAA 451 593 1897 Antisense
AAGAAAAGTTCTGGACCATCTTCAT 172 153 1930 Antisense
CATCTTCATCCAAGGCCATTTCGAA 395 213 1946 Antisense
Sequence Source Affymetrix Proprietary Database