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[174818_at] helicase

Description CEK025D7R_rc /REP_DB=TREMBL Accession /GB=D33049 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk25d7 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 17      4grp_highest_8_8 > 52      4grp_high_8_8 > 16      6grp_highest_nonorm > 11      6grp_total > 06      4grp_total > 39      6grp_highest_sub > De      6grp_cgc > 13      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 1578
1 2 3 4 range
A 2781.5
(3)
P 		1469.7
(-3)
P 		1528.1
(-2.7)
P 		1923.9
(-0.9)
P 		1312
B 2989.7
(3)
P 		1549.2
(-2.5)
P 		1412.1
(-3)
P 		1884.1
(-1.2)
P 		1578
C 2863.4
(3)
P 		1714.2
(-2.7)
P 		1656.8
(-3)
P 		2257.4
(-0)
P 		1207
avr 2878.2
(3) 		1577.7
(-2.8) 		1532.3
(-3) 		2021.8
(-0.8) 		1346

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1475
1 2 3 4 5 6 range
A 2457.9
(3)
P 		1878.4
(0.6)
P 		1241.6
(-2)
P 		985.8
(-3)
P 		1398.6
(-1.3)
P 		1161.8
(-2.3)
P 		1472
B 2461
(3)
P 		1780.4
(-0)
P 		1159.4
(-2.8)
P 		1558.1
(-1)
P 		1106.1
(-3)
P 		1243.6
(-2.4)
P 		1355
C 2117.9
(3)
P 		1667.7
(0.6)
P 		1340
(-1.2)
P 		997.2
(-3)
P 		1207.8
(-1.9)
P 		1015.5
(-2.9)
P 		1121
avr 2345.6
(3) 		1775.5
(0.2) 		1247
(-2.5) 		1180.4
(-2.8) 		1237.5
(-2.5) 		1140.3
(-3) 		1205
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 731
1 2 3 4 range
A 1012.8
(3)
P 		319
(-2.7)
P 		399.5
(-2)
P 		281.6
(-3)
P 		731
B 953.4
(3)
P 		382.6
(-2.5)
P 		327.2
(-3)
P 		401.5
(-2.3)
P 		626
C 947.9
(3)
P 		492.9
(-1.8)
P 		577.4
(-0.9)
P 		380.6
(-3)
P 		567
avr 971.4
(3) 		398.2
(-2.6) 		434.7
(-2.2) 		354.6
(-3) 		617

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 656
1 2 3 4 5 6 range
A 453.1
(-0.1)
P 		668
(3)
P 		270.4
(-2.7)
P 		250
(-3)
P 		422
(-0.5)
P 		282.9
(-2.5)
P 		418
B 856.3
(3)
P 		592.6
(0.2)
P 		281.5
(-3)
P 		412.7
(-1.6)
P 		449.4
(-1.2)
P 		463.7
(-1.1)
P 		575
C 785
(3)
P 		508.9
(0.2)
P 		341.1
(-1.6)
P 		200.5
(-3)
P 		390.8
(-1)
P 		339.9
(-1.6)
P 		585
avr 698.1
(3) 		589.8
(1.4) 		297.7
(-2.9) 		287.7
(-3) 		420.7
(-1.1) 		362.2
(-1.9) 		410
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174818_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20333
Sequence Type Exemplar sequence
Representative Public ID CEK025D7R NCBI
Target Description CEK025D7R_rc /REP_DB=TREMBL Accession /GB=D33049 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk25d7 : 3prime end, single read.
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_059025(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059025 NCBI Caenorhabditis elegans T04D1.4 (helicase) mRNA, complete cds. 11/11 None
T04D1.4 ENSEMBL cdna:known chromosome:CEL140:I:4685875:4697868:-1 gene:T04D1.4 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
chrI:4685904-4686256(-) 100.0 100.0
Public Domain and Genome References
Gene Title helicase
Ensembl T04D1.4
Entrez Gene 172079 Entrez gene
SwissProt O61845 EMBL-EBI
WormBase CE18196 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1596142_AT chromodomain helicase DNA binding protein 7 cfa
CANINE_2:CFA.1799.1.A1_S_AT chromodomain helicase DNA binding protein 7 cfa
CANINE_2:CFAAFFX.11615.1.S1_S_AT chromodomain helicase DNA binding protein 7 cfa
CANINE_2:CFAAFFX.11619.1.S1_AT chromodomain helicase DNA binding protein 7 cfa
CANINE_2:CFAAFFX.11633.1.S1_S_AT chromodomain helicase DNA binding protein 7 cfa
CANINE_2:CFAAFFX.11648.1.S1_AT chromodomain helicase DNA binding protein 7 cfa
CHICKEN:GGA.7719.1.S1_S_AT chromodomain helicase DNA binding protein 7 gga
CHICKEN:GGAAFFX.20690.1.S1_S_AT chromodomain helicase DNA binding protein 7 gga
CHICKEN:GGAAFFX.24689.1.S1_AT chromodomain helicase DNA binding protein 7 gga
CHICKEN:GGAAFFX.9854.1.S1_AT chromodomain helicase DNA binding protein 7 gga
CHICKEN:GGAAFFX.9854.2.S1_S_AT chromodomain helicase DNA binding protein 7 gga
CHICKEN:GGAAFFX.9854.3.S1_S_AT chromodomain helicase DNA binding protein 7 gga
HG-U133_PLUS_2:226123_AT chromodomain helicase DNA binding protein 7 hs
HG-U133B:226123_AT chromodomain helicase DNA binding protein 7 hs
HG-U133_PLUS_2:220619_AT chromodomain helicase DNA binding protein 7 hs
HG-U133A:220619_AT chromodomain helicase DNA binding protein 7 hs
HG-U133A_2:220619_AT chromodomain helicase DNA binding protein 7 hs
HU35KSUBA:N29076_AT chromodomain helicase DNA binding protein 7 hs
HU35KSUBC:RC_AA259140_AT chromodomain helicase DNA binding protein 7 hs
HG-U133A:218829_S_AT chromodomain helicase DNA binding protein 7 hs
HG-U133_PLUS_2:218829_S_AT chromodomain helicase DNA binding protein 7 hs
HG-U133A_2:218829_S_AT chromodomain helicase DNA binding protein 7 hs
U133_X3P:G8923329_3P_A_AT chromodomain helicase DNA binding protein 7 hs
U133_X3P:G11034826_3P_AT chromodomain helicase DNA binding protein 7 hs
U133_X3P:HS.60238.0.A1_3P_AT chromodomain helicase DNA binding protein 7 hs
U133_X3P:HS.105461.0.A1_3P_A_AT chromodomain helicase DNA binding protein 7 hs
HG-U133_PLUS_2:222755_S_AT chromodomain helicase DNA binding protein 7 hs
HG-U133B:222755_S_AT chromodomain helicase DNA binding protein 7 hs
HG-U95B:42567_AT chromodomain helicase DNA binding protein 7 hs
HG-U95C:62491_AT chromodomain helicase DNA binding protein 7 hs
HG-U95E:74491_AT chromodomain helicase DNA binding protein 7 hs
HG-U95E:77501_AT chromodomain helicase DNA binding protein 7 hs
HG-U95E:89743_AT chromodomain helicase DNA binding protein 7 hs
HG-U95C:55377_AT Chromodomain helicase DNA binding protein 7 hs
HG-U95E:70239_AT Chromodomain helicase DNA binding protein 7 hs
HU35KSUBB:RC_R09557_AT Chromodomain helicase DNA binding protein 7 hs
HU35KSUBD:RC_W78145_AT Chromodomain helicase DNA binding protein 7 hs
MG-U74BV2:113462_AT chromodomain helicase DNA binding protein 7 mm
MOE430B:1437745_AT chromodomain helicase DNA binding protein 7 mm
MOUSE430_2:1437745_AT chromodomain helicase DNA binding protein 7 mm
MG-U74AV2:103303_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MG-U74BV2:111619_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MG-U74BV2:113515_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MG-U74CV2:135735_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MG-U74CV2:137571_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOE430B:1441154_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOUSE430_2:1441154_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOUSE430_2:1446621_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOE430B:1446621_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOE430B:1447409_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOUSE430_2:1447409_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOUSE430A_2:1448026_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOE430A:1448026_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MOUSE430_2:1448026_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MU11KSUBA:AA289572_S_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
MU19KSUBA:TC23295_AT Chromodomain helicase DNA binding protein 7 (Chd7), mRNA mm
RAE230B:1378361_AT chromodomain helicase DNA binding protein 7 (predicted) rn
RAT230_2:1378361_AT chromodomain helicase DNA binding protein 7 (predicted) rn
RAE230B:1382504_AT chromodomain helicase DNA binding protein 7 (predicted) rn
RAT230_2:1382504_AT chromodomain helicase DNA binding protein 7 (predicted) rn
RAE230B:1378411_AT Chromodomain helicase DNA binding protein 7 (predicted) rn
RAT230_2:1378411_AT Chromodomain helicase DNA binding protein 7 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6333 chromatin assembly or disassembly 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
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
Protein Similarities
Method ID Description E-Value
blast AAC17559 Hypothetical protein T04D1.4 [Caenorhabditis elegans] ref|NP_491426.1| T04D1.4 [Caenorhabditis elegans] 0.0
blast CAE74540 Hypothetical protein CBG22297 [Caenorhabditis briggsae] 0.0
blast NP_060250 chromodomain helicase DNA binding protein 7 [Homo sapiens] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.1.Myb All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Myb 1.70000004768372
Pfam IPR000330 EMBL-EBI SNF2 related domain 3.0E-105
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 2.1E-25
Sequence
Target Sequence 
>C. ELEGANS:174818_AT
ttcatccgcacacatttttctcatgtaatgggtaatctacctggccgggatttcacatta
caaatcgaaaaaacaaactggtgcaaatctttccctctcagaaaattatctctctatctc
ttttttcatttttctctctctttccaatcgggcaactttatttttagacaagatgtgaga
ttttatgtattttttgattcaacctactctctcacaccgaaactctccttctatccattc
ttgttttattaatgtgatctctggaatatacctattatcttcaactcttcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCATCCGCACACATTTTTCTCATG 459 687 27 Antisense
GTAATGGGTAATCTACCTGGCCGGG 451 455 51 Antisense
TACCTGGCCGGGATTTCACATTACA 261 651 64 Antisense
ACAAACTGGTGCAAATCTTTCCCTC 512 111 99 Antisense
GCAAATCTTTCCCTCTCAGAAAATT 539 317 109 Antisense
AAATTATCTCTCTATCTCTTTTTTC 694 115 129 Antisense
CTCTCTTTCCAATCGGGCAACTTTA 615 229 162 Antisense
TTTTTTGATTCAACCTACTCTCTCA 27 677 216 Antisense
TCCTTCTATCCATTCTTGTTTTATT 102 593 252 Antisense
TAATGTGATCTCTGGAATATACCTA 78 637 276 Antisense
TATACCTATTATCTTCAACTCTTCC 380 659 293 Antisense
Sequence Source Affymetrix Proprietary Database