[Home] | [Total List]

[192145_s_at] 'Cold-shock' DNA-binding domain

Description F33A8.3 /REP_DB=WormBase Gene ID /WP=CE17755 /TR=O62213 /GB=CAB04257.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Cold-shock DNA-binding domain
Cluster 6grp_highest_10_10 > 31      6grp_high1_10_10 > 03      4grp_highest_8_8 > 41      4grp_high_8_8 > 42      6grp_highest_nonorm > 12      6grp_total > 24      4grp_total > 53      6grp_highest_sub > De      6grp_cgc > 31      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1506
1 2 3 4 range
A 2463.2
(3)
P 		2090.6
(1)
P 		1796.1
(-0.6)
P 		1363.3
(-3)
P 		1100
B 2729
(3)
P 		2189
(0.6)
P 		1953.3
(-0.4)
P 		1358.4
(-3)
P 		1371
C 2415.6
(3)
P 		2033.2
(1.1)
P 		1984.8
(0.8)
P 		1223.4
(-3)
P 		1192
avr 2535.9
(3) 		2104.3
(0.9) 		1911.4
(-0.1) 		1315
(-3) 		1221

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1755
1 2 3 4 5 6 range
A 1828.2
(-0.5)
P 		2555.5
(3)
P 		1765.8
(-0.8)
P 		2081.2
(0.7)
P 		1313.5
(-3)
P 		1693.2
(-1.2)
P 		1242
B 2116.8
(3)
P 		1866.3
(0.9)
P 		1787.4
(0.3)
P 		1573.3
(-1.5)
P 		1538.6
(-1.8)
P 		1395.2
(-3)
P 		722
C 2967.4
(3)
P 		1837
(-0.9)
P 		2396.8
(1)
P 		1437.5
(-2.2)
P 		1781.1
(-1.1)
P 		1212.9
(-3)
P 		1755
avr 2304.1
(3) 		2086.3
(1.5) 		1983.3
(0.8) 		1697.3
(-1.2) 		1544.4
(-2.2) 		1433.8
(-3) 		870
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 697
1 2 3 4 range
A 896.9
(3)
P 		453.8
(-0.8)
P 		469.5
(-0.7)
P 		199.6
(-3)
P 		697
B 870.3
(3)
P 		540.6
(-0.4)
P 		452.6
(-1.3)
P 		289.5
(-3)
P 		581
C 799.6
(3)
P 		584.6
(0.8)
P 		691.8
(1.9)
P 		206.3
(-3)
P 		593
avr 855.6
(3) 		526.3
(-0.2) 		538
(-0.1) 		231.8
(-3) 		624

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 811
1 2 3 4 5 6 range
A 337
(-3)
P 		908.9
(3)
P 		384.5
(-2.5)
P 		527.8
(-1)
P 		396.4
(-2.4)
P 		412.2
(-2.2)
P 		572
B 736.5
(3)
P 		621.2
(0.8)
P 		434
(-2.7)
P 		416.7
(-3)
P 		625.1
(0.9)
P 		520.3
(-1.1)
P 		320
C 1099.9
(3)
P 		560.5
(-1)
P 		610
(-0.6)
P 		289.1
(-3)
P 		576.3
(-0.9)
P 		406
(-2.1)
P 		811
avr 724.5
(3) 		696.9
(2.5) 		476.2
(-1.8) 		411.2
(-3) 		532.6
(-0.7) 		446.2
(-2.3) 		313
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192145_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3256
Sequence Type Exemplar sequence
Representative Public ID F33A8.3 NCBI
Target Description F33A8.3 /REP_DB=WormBase Gene ID /WP=CE17755 /TR=O62213 /GB=CAB04257.1 /SUBMIT=HINXTON /CHR=2 /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_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
SNAP00000001852 ENSEMBL cdna:SNAP chromosome:CEL140:II:11039936:11041270:-1 11/11 None
GENEFINDER00000001877 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11039936:11045662:-1 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:11039932-11041037(-) 88.84 100.0
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 CAB04257 Hypothetical protein F33A8.3 [Caenorhabditis elegans] ref|NP_496366.1| C.Elegans Y-box family member (cey-1) [Caenorhabditis elegans] 4.0E-65
blast CAB04257 Hypothetical protein F33A8.3 [Caenorhabditis elegans] ref|NP_496366.1| C.Elegans Y-box family member (cey-1) [Caenorhabditis elegans] 2.0E-64
blast CAE59581 Hypothetical protein CBG02981 [Caenorhabditis briggsae] 2.0E-59
blast CAE59581 Hypothetical protein CBG02981 [Caenorhabditis briggsae] 3.0E-59
blast CAE59581 Hypothetical protein CBG02981 [Caenorhabditis briggsae] 1.0E-58
Protein Domains
Database ID Description E-Value
Pfam IPR002059 EMBL-EBI Cold-shock DNA-binding domain 1.4E-36
Pfam IPR002059 EMBL-EBI Cold-shock DNA-binding domain 1.4E-36
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0011
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-4
Pfam IPR002059 EMBL-EBI Cold-shock DNA-binding domain 1.4E-36
Sequence
Target Sequence 
>C. ELEGANS:192145_S_AT
gtggcagagcaaccagctgacaagccagtgaaggctacaaaagtgaagggaacagtgaaa
tggttcaacgttaagaacggatacggattcatcaaccgcactgacaccaacgaagacatc
ttcgtccatcagaccgccatcatcaacaacaacccgaacaagtacttgagaagtcttgga
gacaatgaagaggtcatgttcgacattgtcgaaggatccaagggtctcgaagcggccagc
gtaacaggaccagatggaggaccagttcaaggatccaagtatgctgccgatcgtgatgct
gaaaatgcagcacgtggacgtggtggacgcggacgtggacgacgtggaggacgtggtgga
atccgacacgactctggatcaagagacgccgaggaaggtggtgctccacgtggaggtggt
cgtggtggaagccgtcgtggtggcggtggacgtggtggtggccgtaccaacagtggtgga
gaggagactgctcgtgacacag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGGCAGAGCAACCAGCTGACAAGC 159 491 31 Antisense
TACGGATTCATCAACCGCACTGACA 522 647 112 Antisense
AAGGATCCAAGGGTCTCGAAGCGGC 3 159 242 Antisense
TCGAAGCGGCCAGCGTAACAGGACC 462 585 257 Antisense
TTCAAGGATCCAAGTATGCTGCCGA 312 683 296 Antisense
TATGCTGCCGATCGTGATGCTGAAA 277 655 310 Antisense
TGGACGCGGACGTGGACGACGTGGA 137 545 354 Antisense
TGGTGGAATCCGACACGACTCTGGA 610 553 384 Antisense
AAGAGACGCCGAGGAAGGTGGTGCT 508 153 411 Antisense
GGTGGCCGTACCAACAGTGGTGGAG 245 497 487 Antisense
GGAGAGGAGACTGCTCGTGACACAG 211 519 508 Antisense
Sequence Source Affymetrix Proprietary Database