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[193596_s_at] helicase-DNA-binding like protein

Description T14G8.1 /REP_DB=WormBase Gene ID /WP=CE03657 /GEN=chd-3 /TR=SW:Q22516 /GB=CAA91810.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=helicase-DNA-binding like protein
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 03      4grp_highest_8_8 > 48      4grp_high_8_8 > 42      6grp_highest_nonorm > 41      6grp_total > 25      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 24      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 477
1 2 3 4 range
A 838.8
(3)
P 		652
(0.7)
P 		528.1
(-0.9)
P 		361.7
(-3)
P 		477
B 750.6
(3)
P 		714.1
(2.3)
P 		533.2
(-1)
P 		427.7
(-3)
P 		323
C 822.3
(3)
P 		699.2
(1.4)
P 		642.2
(0.6)
P 		370
(-3)
P 		452
avr 803.9
(3) 		688.4
(1.3) 		567.8
(-0.4) 		386.5
(-3) 		417

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 589
1 2 3 4 5 6 range
A 820.6
(1.7)
P 		891.9
(3)
P 		651.5
(-1.5)
P 		570.1
(-3)
P 		568.7
(-3)
P 		615
(-2.1)
P 		323
B 782
(3)
P 		755.2
(2.5)
P 		669.2
(1.1)
P 		596.7
(-0.1)
P 		424.8
(-3)
P 		561.5
(-0.7)
P 		357
C 1013.9
(3)
P 		756.7
(-0)
P 		697.4
(-0.7)
P 		503.7
(-3)
P 		506.3
(-3)
P 		505.1
(-3)
P 		510
avr 872.2
(3) 		801.3
(1.9) 		672.7
(-0.2) 		556.8
(-2.1) 		499.9
(-3) 		560.5
(-2) 		372
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 253
1 2 3 4 range
A 305.4
(3)
P 		141.5
(-0.9)
P 		138.1
(-1)
P 		52.9
(-3)
P 		253
B 239.4
(3)
P 		176.4
(0.5)
P 		123.5
(-1.7)
P 		91.1
(-3)
P 		148
C 272.2
(3)
P 		201
(1)
P 		223.8
(1.6)
P 		62.4
(-3)
P 		210
avr 272.3
(3) 		173
(0.1) 		161.8
(-0.3) 		68.8
(-3) 		204

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 275
1 2 3 4 5 6 range
A 151.3
(-2.7)
P 		317.2
(3)
P 		141.9
(-3)
P 		144.6
(-2.9)
P 		171.6
(-2)
P 		149.7
(-2.7)
P 		175
B 272.1
(3)
P 		251.4
(1.9)
P 		162.5
(-2.8)
P 		158
(-3)
P 		172.6
(-2.2)
P 		209.4
(-0.3)
P 		114
C 375.8
(3)
P 		230.9
(-0.2)
P 		177.5
(-1.3)
P 		101.3
(-3)
P 		163.8
(-1.6)
P 		169.1
(-1.5)
P 		275
avr 266.4
(3) 		266.5
(3) 		160.6
(-1.8) 		134.6
(-3) 		169.3
(-1.4) 		176.1
(-1.1) 		132
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193596_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17529
Sequence Type Exemplar sequence
Representative Public ID T14G8.1 NCBI
Target Description T14G8.1 /REP_DB=WormBase Gene ID /WP=CE03657 /GEN=chd-3 /TR=SW:Q22516 /GB=CAA91810.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=helicase-DNA-binding like 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_077739(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077739 NCBI Caenorhabditis elegans CHromoDomain protein family member (chd-3) (chd-3) mRNA, complete cds. 11/11 None
SNAP00000007532 ENSEMBL cdna:SNAP chromosome:CEL140:X:12846781:12852502:-1 10/11 None
GENEFINDER00000007538 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12846781:12852502:-1 10/11 None
T14G8.1 ENSEMBL cdna:known chromosome:CEL140:X:12846352:12852520:-1 gene:T14G8.1 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
chrX:12846536-12852502(-) 100.0 100.0
Public Domain and Genome References
Gene Title helicase-DNA-binding like protein
Gene Symbol chd-3
Ensembl T14G8.1
Entrez Gene 181421 Entrez gene
SwissProt Q22516 EMBL-EBI
WormBase CE03657 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.29898.1.S1_AT similar to chromodomain helicase DNA binding protein 5 cfa
CANINE_2:CFAAFFX.29898.1.S1_S_AT similar to chromodomain helicase DNA binding protein 5 cfa
CANINE_2:CFAAFFX.29905.1.S1_S_AT similar to chromodomain helicase DNA binding protein 5 cfa
CHICKEN:GGAAFFX.488.2.S1_S_AT similar to chromodomain helicase DNA binding protein 5 gga
CHICKEN:GGAAFFX.488.5.S1_S_AT similar to chromodomain helicase DNA binding protein 5 gga
HG-U133_PLUS_2:217250_S_AT chromodomain helicase DNA binding protein 5 hs
HG-U133A_2:217250_S_AT chromodomain helicase DNA binding protein 5 hs
HG-U133A:217250_S_AT chromodomain helicase DNA binding protein 5 hs
HU35KSUBA:RC_AA435597_AT chromodomain helicase DNA binding protein 5 hs
HU35KSUBB:RC_R56066_S_AT chromodomain helicase DNA binding protein 5 hs
U133_X3P:HS.158291.1.S1_3P_A_AT chromodomain helicase DNA binding protein 5 hs
U133_X3P:HS.158291.0.S1_3P_S_AT chromodomain helicase DNA binding protein 5 hs
HG-U133A_2:213965_S_AT chromodomain helicase DNA binding protein 5 hs
HG-U133_PLUS_2:213965_S_AT chromodomain helicase DNA binding protein 5 hs
HG-U133A:213965_S_AT chromodomain helicase DNA binding protein 5 hs
HG-U95AV2:32093_AT chromodomain helicase DNA binding protein 5 hs
U133_X3P:HS2.376391.1.S1_3P_AT Chromodomain helicase DNA binding protein 5 hs
HG-U133_PLUS_2:1564660_AT Chromodomain helicase DNA binding protein 5 hs
MOUSE430_2:1436095_AT chromodomain helicase DNA binding protein 5 mm
MOE430B:1436095_AT chromodomain helicase DNA binding protein 5 mm
MG-U74CV2:138468_AT chromodomain helicase DNA binding protein 5 mm
MG-U74BV2:110170_AT chromodomain helicase DNA binding protein 5 mm
MU19KSUBA:TC15457_AT Chromodomain helicase DNA binding protein 5, mRNA (cDNA clone MGC:107722 IMAGE:6847152) mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6333 chromatin assembly or disassembly inferred from electronic annotation QuickGO AmiGO
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
118 histone deacetylase complex inferred from sequence similarity QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3682 chromatin binding inferred from electronic annotation QuickGO AmiGO
4386 helicase activity inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
8026 ATP-dependent helicase activity inferred from electronic annotation QuickGO AmiGO
3678 DNA helicase activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA91810 Hypothetical protein T14G8.1 [Caenorhabditis elegans] emb|CAA91798.1| Hypothetical protein T14G8.1 [Caenorhabditis elegans] ref|NP_510140.1| CHromoDomain protein family member (chd-3) [Caenorhabditis elegans] gb|AAG29837.1| CHD-3 [Caenorhabditis elegans] sp|Q22516|CHD3_CAEEL Chromodomain helicase-DNA-binding protein 3 homolog (CHD-3) 0.0
blast NP_504523 LEThal family member (let-418) [Caenorhabditis elegans] gb|AAC25894.1| Lethal protein 418 [Caenorhabditis elegans] gb|AAG29838.1| LET-418 [Caenorhabditis elegans] 0.0
blast CAE64562 Hypothetical protein CBG09312 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR009463 EMBL-EBI Protein of unknown function DUF1087 1.4E-30
Pfam IPR000330 EMBL-EBI SNF2 related domain 1.6E-103
Pfam IPR001965 EMBL-EBI Zn-finger-like, PHD finger 8.9E-19
Pfam IPR001965 EMBL-EBI Zn-finger-like, PHD finger 1.2E-22
Pfam IPR000953 EMBL-EBI Chromo 1.2E-6
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.2E-26
Pfam IPR009462 EMBL-EBI Protein of unknown function DUF1086 2.2E-99
Pfam IPR009463 EMBL-EBI Protein of unknown function DUF1087 1.4E-30
Pfam IPR000330 EMBL-EBI SNF2 related domain 1.6E-103
Pfam IPR000953 EMBL-EBI Chromo 1.2E-6
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.2E-26
Pfam IPR009462 EMBL-EBI Protein of unknown function DUF1086 2.2E-99
Sequence
Target Sequence 
>C. ELEGANS:193596_S_AT
aacttctcgagcaatcactggtcattgaagaacaacttcgtcgtgcagctcacatcaaca
aacaacagtctcctgaccaagttggccaattggctcagcatttctcggagctggagcaca
ctgctgatgctcacgtcaatattgcaagagaaagcaacaatggaaacagaaatgctaacg
cgattcttcacaagtgccttgcccaactcgatgatttgctttccgacttgaaaaccgacg
ttgcaagactgccagcaacaatctctcaagttcggccagtcaccgaaagacttcaaatga
gtgaacgacaaattctatcgcgcttagtagtcgccaaggatcccgatgctgctccaagca
agccagcactcccaccaagcggaccattcatcacacctttgttcaatcaaaacttcacca
ctatccagccaaagtttccttctctatttgactgtaatttgtcgcctgatgatgaaccta
ttgatattgaaggatcaatatctgcagctgtcgcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACTTCTCGAGCAATCACTGGTCAT 197 139 4748 Antisense
GAAGAACAACTTCGTCGTGCAGCTC 527 339 4774 Antisense
GCCAATTGGCTCAGCATTTCTCGGA 297 277 4832 Antisense
TAACGCGATTCTTCACAAGTGCCTT 556 637 4923 Antisense
TGCCCAACTCGATGATTTGCTTTCC 118 585 4947 Antisense
GCAACAATCTCTCAAGTTCGGCCAG 317 317 5002 Antisense
ATCGCGCTTAGTAGTCGCCAAGGAT 584 37 5064 Antisense
GATGCTGCTCCAAGCAAGCCAGCAC 605 413 5092 Antisense
ACCATTCATCACACCTTTGTTCAAT 498 87 5130 Antisense
ACTATCCAGCCAAAGTTTCCTTCTC 226 101 5167 Antisense
AGGATCAATATCTGCAGCTGTCGCC 286 57 5238 Antisense
Sequence Source Affymetrix Proprietary Database