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[189699_at] cytidine deaminase

Description F49E8.4 /REP_DB=WormBase Gene ID /WP=CE10792 /TR=Q20628 /GB=AAB03151.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cytidine deaminase
Cluster 6grp_highest_10_10 > 48      6grp_high1_10_10 > 73      4grp_highest_8_8 > 11      4grp_high_8_8 > 55      6grp_highest_nonorm > 62      6grp_total > 74      4grp_total > 48      6grp_cgc > 76      6grp_high1_sub > 03_04      6grp_cgc_sub > 03_04      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 278
1 2 3 4 range
A 205.5
(-3)
P 		357.5
(0.5)
P 		462.6
(3)
P 		270.7
(-1.5)
P 		257
B 185
(-3)
P 		333.1
(0.9)
P 		411.3
(3)
P 		233.1
(-1.7)
P 		226
C 202.6
(-3)
P 		361.9
(1.3)
P 		426
(3)
P 		212
(-2.7)
P 		223
avr 197.7
(-3) 		350.8
(0.9) 		433.3
(3) 		238.6
(-2) 		236

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 367
1 2 3 4 5 6 range
A 278.5
(-3)
P 		305.8
(-2.4)
P 		575.8
(3)
P 		565.4
(2.8)
P 		491.4
(1.3)
P 		424.5
(-0.1)
P 		297
B 299.5
(-3)
P 		425.2
(-0.8)
P 		645.9
(3)
P 		561
(1.5)
P 		578.2
(1.8)
P 		547.6
(1.3)
P 		346
C 293.4
(-3)
P 		398.9
(-0.6)
P 		521.5
(2.1)
P 		561.8
(3)
P 		423.2
(-0.1)
P 		547.8
(2.7)
P 		268
avr 290.5
(-3) 		376.6
(-1.2) 		581.1
(3) 		562.7
(2.6) 		497.6
(1.3) 		506.6
(1.5) 		291
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 113
1 2 3 4 range
A 74.8
(-0.4)
P 		77.6
(-0.2)
P 		120.9
(3)
P 		39.6
(-3)
P 		81
B 59
(-1.8)
P 		82.3
(1.3)
P 		95.3
(3)
P 		49.7
(-3)
P 		46
C 67.1
(-1.3)
P 		104.1
(0.6)
P 		148.5
(3)
P 		35.8
(-3)
P 		113
avr 67
(-1.1) 		88
(0.5) 		121.6
(3) 		41.7
(-3) 		80

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 184
1 2 3 4 5 6 range
A 51.3
(-3)
P 		108.8
(0.6)
P 		125.4
(1.6)
P 		143.4
(2.7)
P 		148.3
(3)
P 		103.4
(0.2)
P 		97
B 104.2
(-3)
P 		141.5
(-1.3)
P 		156.9
(-0.6)
P 		148.6
(-1)
P 		234.9
(3)
P 		204.2
(1.6)
P 		131
C 108.8
(-3)
P 		121.7
(-2)
P 		132.7
(-1.1)
P 		113
(-2.7)
P 		137
(-0.7)
P 		183.4
(3)
P 		75
avr 88.1
(-3) 		124
(-0.5) 		138.3
(0.5) 		135
(0.3) 		173.4
(3) 		163.7
(2.3) 		85
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189699_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8729
Sequence Type Exemplar sequence
Representative Public ID F49E8.4 NCBI
Target Description F49E8.4 /REP_DB=WormBase Gene ID /WP=CE10792 /TR=Q20628 /GB=AAB03151.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cytidine deaminase
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_068820(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068820 NCBI Caenorhabditis elegans CytiDine Deaminase family member (cdd-2) (cdd-2) mRNA, complete cds. 11/11 None
SNAP00000021359 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7547236:7547877:-1 11/11 None
GENEFINDER00000021369 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7547236:7547877:-1 10/11 None
F49E8.4 ENSEMBL cdna:known chromosome:CEL140:IV:7547127:7547877:-1 gene:F49E8.4 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
chrIV:7547241-7547883(-) 100.0 100.0
Public Domain and Genome References
Gene Title cytidine deaminase
Gene Symbol cdd-2
Ensembl F49E8.4
Entrez Gene 186044 Entrez gene
SwissProt Q20628 EMBL-EBI
WormBase CE10792 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1590945_AT similar to cytidine deaminase cfa
CANINE_2:CFA.14519.1.A1_AT similar to cytidine deaminase cfa
CANINE_2:CFAAFFX.23160.1.S1_AT similar to cytidine deaminase cfa
DROSOPHILA_2:1634429_AT dm
DROSGENOME1:146013_AT dm
HG-U95AV2:1117_AT cytidine deaminase hs
HC-G110:1117_AT cytidine deaminase hs
HG-U133A:205627_AT cytidine deaminase hs
HG-U133A_2:205627_AT cytidine deaminase hs
HG-U133_PLUS_2:205627_AT cytidine deaminase hs
HG-FOCUS:205627_AT cytidine deaminase hs
HUGENEFL:L27943_AT cytidine deaminase hs
U133_X3P:G11386156_3P_AT cytidine deaminase hs
MOUSE430_2:1427357_AT cytidine deaminase mm
MOE430A:1427357_AT cytidine deaminase mm
MOUSE430A_2:1427357_AT cytidine deaminase mm
MG-U74BV2:163731_AT cytidine deaminase mm
MU19KSUBC:TC40483_AT Cytidine deaminase, mRNA (cDNA clone IMAGE:4216440) mm
RG-U34C:RC_AA859352_AT cytidine deaminase (predicted) rn
RAE230A:1377112_AT cytidine deaminase (predicted) rn
RAT230_2:1377112_AT cytidine deaminase (predicted) rn
YEAST_2:1772736_AT Cytidine deaminase; catalyzes the modification of cytidine to uridine in vitro but native RNA substrates have not been identified, localizes to both the nucleus and cytoplasm Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
46087 cytidine metabolism inferred from electronic annotation QuickGO AmiGO
9451 RNA modification inferred from direct assay QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5623 cell inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4126 cytidine deaminase activity inferred from electronic annotation QuickGO AmiGO
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
16787 hydrolase activity inferred from electronic annotation QuickGO AmiGO
4126 cytidine deaminase activity inferred from direct assay QuickGO AmiGO
3723 RNA binding inferred from direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB03151 Cytidine deaminase protein 2 [Caenorhabditis elegans] ref|NP_501221.1| CytiDine Deaminase family member (cdd-2) [Caenorhabditis elegans] 8.0E-89
blast AAB03151 Cytidine deaminase protein 2 [Caenorhabditis elegans] ref|NP_501221.1| CytiDine Deaminase family member (cdd-2) [Caenorhabditis elegans] 5.0E-87
blast CAE61910 Hypothetical protein CBG05906 [Caenorhabditis briggsae] 9.0E-70
blast CAE61910 Hypothetical protein CBG05906 [Caenorhabditis briggsae] 2.0E-68
blast CAE74856 Hypothetical protein CBG22709 [Caenorhabditis briggsae] 3.0E-42
Protein Domains
Database ID Description E-Value
Pfam IPR002125 EMBL-EBI Cytidine/deoxycytidylate deaminase, zinc-binding region 3.1E-38
Pfam IPR002125 EMBL-EBI Cytidine/deoxycytidylate deaminase, zinc-binding region 6.0E-35
Sequence
Target Sequence 
>C. ELEGANS:189699_AT
gtcttcctcaagatatttccgatgtggaactagttcatttggcccgagctgcgatgaaac
gggcacattgcccatacagcaagtttccagttggtgcagcgcttctcactgaatctgggg
aaattgtccagggctgcaatgtcgagaatgcttcatacggtggcactatctgcgctgagc
gtagtgctattgtttctgctgtgtcacaaggatacacgaaattccgtgccattgctgtcg
tcactgagctcagcgaacctgcgtctccctgtggactttgccgtcaatttctagttgaat
tcggtgactataaagttgttgtgggaactgcatctaacaataaaattctcatcacctcaa
ctcgcgctcttcttccatttgctttcactcctgaatcgctcgacacttttga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCTTCCTCAAGATATTTCCGATGT 269 469 26 Antisense
GTGGAACTAGTTCATTTGGCCCGAG 224 485 49 Antisense
GGGCACATTGCCCATACAGCAAGTT 200 493 86 Antisense
AAGTTTCCAGTTGGTGCAGCGCTTC 367 157 106 Antisense
TGTCCAGGGCTGCAATGTCGAGAAT 507 557 150 Antisense
GAATGCTTCATACGGTGGCACTATC 464 331 171 Antisense
GGCACTATCTGCGCTGAGCGTAGTG 133 535 187 Antisense
CACGAAATTCCGTGCCATTGCTGTC 696 197 240 Antisense
ATTGCTGTCGTCACTGAGCTCAGCG 332 7 256 Antisense
TGGACTTTGCCGTCAATTTCTAGTT 78 547 297 Antisense
CTCCTGAATCGCTCGACACTTTTGA 276 235 413 Antisense
Sequence Source Affymetrix Proprietary Database