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[173835_at] 'Cold-shock' DNA-binding domain

Description C69702 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y39A1C.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C69702 /WB_GENE_ID=Y39A1C.3 /WP=CE19148 /CHR=3 /FEA=Genomic Cluster /DEF=Cold-shock DNA-binding domain; C.elegans cDNA clone yk368e2 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 73      6grp_high1_10_10 > 37      4grp_highest_8_8 > 28      4grp_high_8_8 > 31      6grp_highest_nonorm > 38      6grp_total > 17      4grp_total > 40      6grp_highest_sub > Cu      6grp_cgc > 07      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1793
1 2 3 4 range
A 7141.6
(1.9)
P 		6214.4
(-3)
P 		7346.7
(3)
P 		7064.3
(1.5)
P 		1132
B 7392.3
(-0.3)
P 		6902.4
(-3)
P 		8007.7
(3)
P 		7840.9
(2.1)
P 		1105
C 6586.4
(-3)
P 		6961
(-1.1)
P 		7788
(3)
P 		6767.8
(-2.1)
P 		1202
avr 7040.1
(-1) 		6692.6
(-3) 		7714.1
(3) 		7224.3
(0.1) 		1022

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1742
1 2 3 4 5 6 range
A 6185.4
(3)
P 		5446.8
(-1.1)
P 		6184.7
(3)
P 		5115.2
(-3)
P 		5831.4
(1)
P 		5898.4
(1.4)
P 		1070
B 6857.6
(3)
P 		5693.4
(-2.2)
P 		6598.6
(1.8)
P 		5894.7
(-1.3)
P 		5526.3
(-3)
P 		6116.1
(-0.3)
P 		1331
C 5573
(0.6)
P 		5258.9
(-3)
P 		5341.1
(-2.1)
P 		5292
(-2.6)
P 		5785.8
(3)
P 		5676
(1.7)
P 		527
avr 6205.3
(3) 		5466.4
(-2.7) 		6041.5
(1.7) 		5434
(-3) 		5714.5
(-0.8) 		5896.8
(0.6) 		771
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1680
1 2 3 4 range
A 2600.3
(3)
P 		1349
(-1.8)
P 		1920.6
(0.4)
P 		1034.1
(-3)
P 		1566
B 2357.4
(3)
P 		1704.7
(-2.7)
P 		1855.6
(-1.4)
P 		1670.9
(-3)
P 		687
C 2180.3
(1)
P 		2001.3
(0.3)
P 		2714.4
(3)
P 		1141.2
(-3)
P 		1573
avr 2379.3
(3) 		1685
(-0.8) 		2163.5
(1.8) 		1282.1
(-3) 		1097

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1322
1 2 3 4 5 6 range
A 1140.2
(-3)
P 		1937.1
(3)
P 		1346.9
(-1.4)
P 		1297.3
(-1.8)
P 		1759.7
(1.7)
P 		1436.1
(-0.8)
P 		797
B 2386.1
(3)
P 		1895.1
(-0.6)
P 		1602.3
(-2.7)
P 		1561.3
(-3)
P 		2245.3
(2)
P 		2280.7
(2.2)
P 		825
C 2065.7
(3)
P 		1604.6
(0.2)
P 		1359.4
(-1.2)
P 		1064.2
(-3)
P 		1872.2
(1.8)
P 		1900.1
(2)
P 		1002
avr 1864
(2.1) 		1812.3
(1.6) 		1436.2
(-1.8) 		1307.6
(-3) 		1959.1
(3) 		1872.3
(2.2) 		652
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173835_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24292
Sequence Type Exemplar sequence
Representative Public ID C69702 NCBI
Target Description C69702 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y39A1C.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C69702 /WB_GENE_ID=Y39A1C.3 /WP=CE19148 /CHR=3 /FEA=Genomic Cluster /DEF=Cold-shock DNA-binding domain; C.elegans cDNA clone yk368e2 : 5prime 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_066992(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066992 NCBI Caenorhabditis elegans C.Elegans Y-box family member (cey-4) (cey-4) mRNA, complete cds. 11/11 None
Y39A1C.3.2 ENSEMBL cdna:known chromosome:CEL140:III:10866826:10868582:-1 gene:Y39A1C.3 11/11 None
Y39A1C.3.1 ENSEMBL cdna:known chromosome:CEL140:III:10866826:10868580:-1 gene:Y39A1C.3 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:10866846-10868493(-) 100.0 100.0
Public Domain and Genome References
Gene Title 'Cold-shock' DNA-binding domain
Gene Symbol cey-4
Ensembl Y39A1C.3
Entrez Gene 176516 Entrez gene
SwissProt Q9XTJ6 EMBL-EBI
WormBase CE19148 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 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 CAA97783 Hypothetical protein Y39A1C.3 [Caenorhabditis elegans] emb|CAA19509.1| Hypothetical protein Y39A1C.3 [Caenorhabditis elegans] ref|NP_499393.1| C.Elegans Y-box family member (cey-4) [Caenorhabditis elegans] 9.0E-98
blast CAE71391 Hypothetical protein CBG18298 [Caenorhabditis briggsae] 8.0E-70
blast CAE68913 Hypothetical protein CBG14892 [Caenorhabditis briggsae] 1.0E-30
Protein Domains
Database ID Description E-Value
Pfam IPR002059 EMBL-EBI Cold-shock DNA-binding domain 3.6E-22
Sequence
Target Sequence 
>C. ELEGANS:173835_AT
gctaaagcttaggcttctagctgttgacacctaccatcaacttttgttatctaattaaac
accttttgtattgagaacagtcccatttcttgaattgtatagctgatcctttcgaaaagc
ccaaaatttccaaaatttgttctgcacgatttatatccactcagttct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTAAAGCTTAGGCTTCTAGCTGTT 147 303 887 Antisense
TCTAGCTGTTGACACCTACCATCAA 251 611 902 Antisense
GACACCTACCATCAACTTTTGTTAT 302 367 912 Antisense
TTATCTAATTAAACACCTTTTGTAT 73 675 933 Antisense
CACCTTTTGTATTGAGAACAGTCCC 276 193 946 Antisense
GAACAGTCCCATTTCTTGAATTGTA 395 351 961 Antisense
GAATTGTATAGCTGATCCTTTCGAA 628 323 978 Antisense
GCTGATCCTTTCGAAAAGCCCAAAA 409 295 988 Antisense
TTCCAAAATTTGTTCTGCACGATTT 698 699 1014 Antisense
GTTCTGCACGATTTATATCCACTCA 209 443 1025 Antisense
GCACGATTTATATCCACTCAGTTCT 242 315 1030 Antisense
Sequence Source Affymetrix Proprietary Database