[Home] | [Total List]

[192269_s_at] 'Cold-shock' DNA-binding domain

Description Y39A1C.3 /REP_DB=WormBase Gene ID /WP=CE19148 /TR=Q9XTJ6 /GB=CAA97783.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Cold-shock DNA-binding domain
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 43      4grp_highest_8_8 > 08      4grp_high_8_8 > 53      6grp_highest_nonorm > 38      6grp_total > 11      4grp_total > 59      6grp_highest_sub > 02_03      6grp_cgc > 54      6grp_high1_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4885
1 2 3 4 range
A 8599.9
(-0.8)
P 		10685.1
(3)
P 		9825.4
(1.4)
P 		7359.4
(-3)
P 		3326
B 9414.8
(-0.2)
P 		10858.7
(2.4)
P 		11198.2
(3)
P 		7817.9
(-3)
P 		3380
C 8841.6
(1)
P 		10138.5
(3)
P 		9040.5
(1.3)
P 		6313.1
(-3)
P 		3825
avr 8952.1
(0.2) 		10560.8
(3) 		10021.4
(2) 		7163.5
(-3) 		3397

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2445
1 2 3 4 5 6 range
A 6857.6
(0.1)
P 		7489.5
(3)
P 		7080.4
(1.2)
P 		6161.5
(-3)
P 		6239.4
(-2.6)
P 		6461.7
(-1.6)
P 		1328
B 5411.3
(-3)
P 		7118.1
(3)
P 		6925.8
(2.3)
P 		6533.2
(0.9)
P 		6671.8
(1.4)
P 		6338.1
(0.3)
P 		1707
C 6550
(1.1)
P 		7026.3
(2.4)
P 		7233.7
(3)
P 		5175.9
(-2.6)
P 		7048.6
(2.5)
P 		5044.4
(-3)
P 		2189
avr 6273
(-1.5) 		7211.3
(3) 		7080
(2.4) 		5956.9
(-3) 		6653.3
(0.3) 		5948.1
(-3) 		1263
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2086
1 2 3 4 range
A 3131.2
(3)
P 		2319.4
(0.6)
P 		2568.6
(1.4)
P 		1077.3
(-3)
P 		2054
B 3002.3
(3)
P 		2681.8
(1.6)
P 		2594.9
(1.2)
P 		1666
(-3)
P 		1336
C 2926.8
(2.4)
P 		2914.9
(2.3)
P 		3150.9
(3)
P 		1064.5
(-3)
P 		2086
avr 3020.1
(3) 		2638.7
(1.7) 		2771.5
(2.1) 		1269.3
(-3) 		1751

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1670
1 2 3 4 5 6 range
A 1264.1
(-3)
P 		2663.6
(3)
P 		1542
(-1.8)
P 		1562.7
(-1.7)
P 		1882.8
(-0.3)
P 		1573.2
(-1.7)
P 		1400
B 1882.9
(-1.8)
P 		2369.3
(1)
P 		1681.8
(-3)
P 		1730.4
(-2.7)
P 		2710.7
(3)
P 		2363.5
(1)
P 		1029
C 2427.8
(3)
P 		2143.9
(1.8)
P 		1841.1
(0.5)
P 		1040.9
(-3)
P 		2280.8
(2.4)
P 		1688.7
(-0.2)
P 		1387
avr 1858.3
(-0.4) 		2392.3
(3) 		1688.3
(-1.5) 		1444.7
(-3) 		2291.4
(2.4) 		1875.1
(-0.3) 		948
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192269_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8098
Sequence Type Exemplar sequence
Representative Public ID Y39A1C.3 NCBI
Target Description Y39A1C.3 /REP_DB=WormBase Gene ID /WP=CE19148 /TR=Q9XTJ6 /GB=CAA97783.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Cold-shock DNA-binding domain
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_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:10867032-10868492(-) 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:192269_S_AT
gtcaaatggttctccgttcgtggacgctacggattcgttgctcgtgataagccaaccgac
gagaatgaggacttcttcgtccatcagaccgccatcaccaagtcaagcaccattaagttc
tatctcagaactctcgatgacgatgagccagtcgtctttgacattgtcgaaggactcaaa
ggaccagaagccgccaacgtgactggaccagatggggagaatgttcgtggatcgagattc
gctcgtactttgctcacccattggagaacaagaggacgtggtggtgcacgaggacgcggt
ggacgaggacgtggtgctccacgtcagacacgtgaccaggacggagatgagaaagatgag
aaggagaagtcggacaccattgagaatagcggagacggagaaactcgcggaaagcgtcgc
actcgccgccacggaaagctccagccagatgctccatccggcgagaagggagacggtgat
gctgccgctg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCAAATGGTTCTCCGTTCGTGGAC 498 1 289 Antisense
ACGCTACGGATTCGTTGCTCGTGAT 220 91 312 Antisense
GAATGAGGACTTCTTCGTCCATCAG 333 331 351 Antisense
GTCAAGCACCATTAAGTTCTATCTC 63 465 390 Antisense
GAGCCAGTCGTCTTTGACATTGTCG 98 385 433 Antisense
GGACTCAAAGGACCAGAAGCCGCCA 405 525 460 Antisense
CCGCCAACGTGACTGGACCAGATGG 139 263 479 Antisense
GGATCGAGATTCGCTCGTACTTTGC 258 501 517 Antisense
GTACTTTGCTCACCCATTGGAGAAC 406 459 533 Antisense
GTGCTCCACGTCAGACACGTGACCA 429 479 602 Antisense
AAGGGAGACGGTGATGCTGCCGCTG 199 159 754 Antisense
Sequence Source Affymetrix Proprietary Database