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[173932_at] 'Cold-shock' DNA-binding domain

Description AV191141 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F33A8.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV191141 /WB_GENE_ID=F33A8.3 /WP=CE17755 /CHR=2 /FEA=Genomic Cluster /DEF=Cold-shock DNA-binding domain; Caenorhabditis elegans cDNA clone:yk590e1 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 02      6grp_high1_10_10 > 01      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 15      6grp_total > 23      4grp_total > 59      6grp_cgc > 70      6grp_high1_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4503
1 2 3 4 range
A 6352.5
(1.9)
P 		4836.7
(-0.5)
P 		7036.2
(3)
P 		3307.4
(-3)
P 		3729
B 5385.7
(-1.6)
P 		7810.2
(3)
P 		5621.7
(-1.2)
P 		4673.1
(-3)
P 		3137
C 6193.7
(1.7)
P 		6948.1
(3)
P 		6934.7
(3)
P 		3345.7
(-3)
P 		3602
avr 5977.3
(1.8) 		6531.7
(3) 		6530.9
(3) 		3775.4
(-3) 		2756

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4905
1 2 3 4 5 6 range
A 5206.2
(-0.5)
P 		6216.6
(3)
P 		5486
(0.5)
P 		4508.2
(-2.9)
P 		4803.7
(-1.9)
P 		4481.8
(-3)
P 		1735
B 6632
(3)
P 		5885.1
(1.1)
P 		5443.2
(-0)
P 		5854.6
(1)
P 		4484.8
(-2.4)
P 		4261.6
(-3)
P 		2370
C 8292.7
(3)
P 		5286.5
(-0.7)
P 		7274.3
(1.8)
P 		5700.8
(-0.2)
P 		5493.4
(-0.4)
P 		3387.8
(-3)
P 		4905
avr 6710.3
(3) 		5796.1
(0.9) 		6067.8
(1.6) 		5354.5
(-0.1) 		4927.3
(-1) 		4043.7
(-3) 		2667
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1933
1 2 3 4 range
A 2313
(3)
P 		1049.9
(-1.1)
P 		1839.4
(1.4)
P 		484.1
(-3)
P 		1829
B 1717.5
(1.6)
P 		1928.9
(3)
P 		1302.7
(-1)
P 		995.8
(-3)
P 		933
C 2050.3
(1.8)
P 		1997.6
(1.6)
P 		2417
(3)
P 		564.1
(-3)
P 		1853
avr 2026.9
(3) 		1658.8
(1.4) 		1853
(2.2) 		681.3
(-3) 		1346

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2114
1 2 3 4 5 6 range
A 959.7
(-3)
P 		2210.9
(3)
P 		1194.7
(-1.9)
P 		1143.4
(-2.1)
P 		1449.6
(-0.7)
P 		1091.2
(-2.4)
P 		1251
B 2307.6
(3)
P 		1958.9
(0.9)
P 		1321.8
(-3)
P 		1550.7
(-1.6)
P 		1822.1
(0)
P 		1589.1
(-1.4)
P 		986
C 3073.7
(3)
P 		1613.1
(-1.5)
P 		1851.4
(-0.8)
P 		1146.4
(-3)
P 		1777.6
(-1)
P 		1134.1
(-3)
P 		1940
avr 2113.7
(3) 		1927.6
(1.7) 		1456
(-1.7) 		1280.2
(-2.9) 		1683.1
(-0.1) 		1271.5
(-3) 		842
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173932_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23192
Sequence Type Exemplar sequence
Representative Public ID AV191141 NCBI
Target Description AV191141 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F33A8.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV191141 /WB_GENE_ID=F33A8.3 /WP=CE17755 /CHR=2 /FEA=Genomic Cluster /DEF=Cold-shock DNA-binding domain; Caenorhabditis elegans cDNA clone:yk590e1 : 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_063965(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063965 NCBI Caenorhabditis elegans C.Elegans Y-box family member (cey-1) (cey-1) mRNA, complete cds. 11/11 None
F33A8.3.1 ENSEMBL cdna:known chromosome:CEL140:II:11039323:11041121:-1 gene:F33A8.3 11/11 None
F33A8.3.2 ENSEMBL cdna:known chromosome:CEL140:II:11039324:11041119:-1 gene:F33A8.3 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
chrII:11039330-11041038(-) 94.31 100.0
Public Domain and Genome References
Gene Title 'Cold-shock' DNA-binding domain
Gene Symbol cey-1
Ensembl F33A8.3
Entrez Gene 174690 Entrez gene
SwissProt O62213 EMBL-EBI
WormBase CE17755 Wormbase
Functional Annotations
Ortholog
ID Title Organism
HG-U133_PLUS_2:201161_S_AT cold shock domain protein A hs
HG-U133A:201161_S_AT cold shock domain protein A hs
HG-U133A_2:201161_S_AT cold shock domain protein A hs
HG-U133_PLUS_2:201160_S_AT cold shock domain protein A hs
HG-U133A_2:201160_S_AT cold shock domain protein A hs
HG-FOCUS:201160_S_AT cold shock domain protein A hs
HG-U133A:201160_S_AT cold shock domain protein A hs
HUGENEFL:X95325_S_AT cold shock domain protein A hs
HUGENEFL:M24069_AT cold shock domain protein A hs
U133_X3P:G4503070_3P_A_AT cold shock domain protein A hs
HG-U95AV2:39839_AT cold shock domain protein A hs
HG-U95E:74763_AT cold shock domain protein A hs
HG-U95D:89690_AT Cold shock domain protein A hs
HU35KSUBC:RC_AA018222_AT Cold shock domain protein A hs
U133_X3P:HS.1139.1.A1_3P_AT Cold shock domain protein A hs
MOUSE430_2:1435800_A_AT cold shock domain protein A mm
MOUSE430A_2:1435800_A_AT cold shock domain protein A mm
MOE430A:1435800_A_AT cold shock domain protein A mm
MG-U74AV2:95755_AT cold shock domain protein A mm
MOE430A:1451012_A_AT cold shock domain protein A mm
MOUSE430A_2:1451012_A_AT cold shock domain protein A mm
MOUSE430_2:1451012_A_AT cold shock domain protein A mm
MU11KSUBA:L35549_RC_AT cold shock domain protein A mm
MG-U74BV2:116030_AT Cold shock domain protein A (Csda), mRNA mm
MU19KSUBA:TC14929_AT Cold shock domain protein A (Csda), mRNA mm
MU19KSUBB:TC34607_S_AT Cold shock domain protein A (Csda), mRNA mm
RG-U34A:D28557_S_AT cold shock domain protein A rn
RAE230A:1370376_A_AT cold shock domain protein A rn
RAT230_2:1370376_A_AT cold shock domain protein A rn
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 CAB04257 Hypothetical protein F33A8.3 [Caenorhabditis elegans] ref|NP_496366.1| C.Elegans Y-box family member (cey-1) [Caenorhabditis elegans] 3.0E-65
blast CAE59581 Hypothetical protein CBG02981 [Caenorhabditis briggsae] 2.0E-59
blast XP_612661 PREDICTED: similar to muscle Y-box protein YB2 [Bos taurus] 5.0E-36
Protein Domains
Database ID Description E-Value
Pfam IPR002059 EMBL-EBI Cold-shock DNA-binding domain 1.4E-36
Sequence
Target Sequence 
>C. ELEGANS:173932_AT
gcgaggcctaagtaattttccagtaaccagtaacactcgtagtaattaagagagcaacta
ggtttttatttcaacccccaactcccccaattcatctcgccacacacacacccacaactt
tgaactttcgctatattacattttcccttattctttcttctttcttttgttttcctaact
cgtgaattattattgcagtacagttactttaagctccccctctaaaacacgtcacaacct
gaatcattctcgtaattaaaccattctcctcccaacaaaaaaatatataattctacctgt
ttcgctttcggatttccaaaacttttcttgtaacaccatcaacaccgaaaatctctgtaa
ttcaacaagcaagcacccacacacacacaccagaccaactgatgacttcccatcttgttt
ttttgtgttgctctgtctttctgagagtatattgctaacagaaaaacgagaaagcataat
atatctgtaccctttcccccttttttgagagaatctttaatgttcaagtacctcttcgcc
cttcatcttgaaatag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCGAGGCCTAAGTAATTTTCCAGTA 339 277 630 Antisense
TTTCCAGTAACCAGTAACACTCGTA 651 613 646 Antisense
CACACCCACAACTTTGAACTTTCGC 690 193 736 Antisense
GAACTTTCGCTATATTACATTTTCC 590 349 751 Antisense
TCTTTTGTTTTCCTAACTCGTGAAT 281 615 792 Antisense
GCAGTACAGTTACTTTAAGCTCCCC 693 309 824 Antisense
CACGTCACAACCTGAATCATTCTCG 500 199 857 Antisense
TCTCGTAATTAAACCATTCTCCTCC 273 607 877 Antisense
ATAATTCTACCTGTTTCGCTTTCGG 149 25 916 Antisense
TTTAATGTTCAAGTACCTCTTCGCC 167 673 1145 Antisense
CTCTTCGCCCTTCATCTTGAAATAG 77 231 1161 Antisense
Sequence Source Affymetrix Proprietary Database