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[191063_at] DNA polymerase family B

Description F10C2.4 /REP_DB=WormBase Gene ID /WP=CE09308 /TR=SW:P90829 /GB=CAB04077.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=DNA polymerase family B
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 77      4grp_highest_8_8 > 35      4grp_high_8_8 > 48      6grp_highest_nonorm > 96      6grp_total > 78      4grp_total > 63      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 407
1 2 3 4 range
A 866
(3)
P 		545.9
(-3)
P 		708.6
(0)
P 		583.2
(-2.3)
P 		320
B 953.3
(3)
P 		640
(-2.2)
P 		681
(-1.6)
P 		594.8
(-3)
P 		359
C 808
(3)
P 		646.3
(-2.8)
P 		794.7
(2.5)
P 		641.9
(-3)
P 		166
avr 875.8
(3) 		610.7
(-2.9) 		728.1
(-0.3) 		606.6
(-3) 		269

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 773
1 2 3 4 5 6 range
A 773.1
(-1.1)
P 		794
(-0.9)
P 		590.1
(-3)
P 		845.8
(-0.4)
P 		929.1
(0.4)
P 		1180.8
(3)
P 		591
B 765.4
(-2)
P 		705.6
(-2.6)
P 		660.1
(-3)
P 		766.2
(-2)
P 		709.2
(-2.5)
P 		1311.9
(3)
P 		652
C 696.8
(-2.5)
P 		657.7
(-2.8)
P 		631.3
(-3)
P 		679.2
(-2.6)
P 		868.1
(-1.1)
P 		1362.8
(3)
P 		732
avr 745.1
(-1.9) 		719.1
(-2.2) 		627.2
(-3) 		763.7
(-1.8) 		835.5
(-1.1) 		1285.2
(3) 		658
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 230
1 2 3 4 range
A 315.3
(3)
P 		118.5
(-2.1)
P 		185.2
(-0.4)
P 		85.4
(-3)
P 		230
B 304
(3)
P 		158.1
(-1.9)
P 		157.8
(-2)
P 		126.8
(-3)
P 		177
C 267.5
(2.7)
P 		185.8
(-0.2)
P 		277
(3)
P 		108.2
(-3)
P 		169
avr 295.6
(3) 		154.1
(-1.5) 		206.7
(0.2) 		106.8
(-3) 		189

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 361
1 2 3 4 5 6 range
A 142.5
(-2.5)
P 		282.4
(2.8)
P 		128.5
(-3)
P 		214.5
(0.2)
P 		280.4
(2.7)
P 		287.5
(3)
P 		159
B 266.3
(-1.1)
P 		234.9
(-1.6)
P 		160.3
(-3)
P 		202.9
(-2.2)
P 		288.2
(-0.7)
P 		489.2
(3)
P 		329
C 258.3
(-0.7)
P 		200.7
(-1.8)
P 		160.7
(-2.5)
P 		136.6
(-3)
P 		280.9
(-0.3)
P 		456.2
(3)
P 		320
avr 222.4
(-1.3) 		239.3
(-0.9) 		149.8
(-3) 		184.7
(-2.2) 		283.2
(0.1) 		411
(3) 		261
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191063_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13402
Sequence Type Exemplar sequence
Representative Public ID F10C2.4 NCBI
Target Description F10C2.4 /REP_DB=WormBase Gene ID /WP=CE09308 /TR=SW:P90829 /GB=CAB04077.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=DNA polymerase family B
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_073616(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073616 NCBI Caenorhabditis elegans F10C2.4 (F10C2.4) mRNA, complete cds. 11/11 None
SNAP00000025559 ENSEMBL cdna:SNAP chromosome:CEL140:V:12044198:12047794:1 11/11 None
GENEFINDER00000025565 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12044198:12047794:1 11/11 None
F10C2.4 ENSEMBL cdna:known chromosome:CEL140:V:12044195:12047909:1 gene:F10C2.4 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
chrV:12044197-12047794(+) 100.0 100.0
Public Domain and Genome References
Gene Title DNA polymerase family B
Ensembl F10C2.4
Entrez Gene 179652 Entrez gene
SwissProt P90829 EMBL-EBI
WormBase CE09308 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247311_AT DNA-directed DNA polymerase delta catalytic subunit, putative (POLD1) at
CANINE_2:CFAAFFX.5353.1.S1_AT similar to DNA polymerase delta catalytic subunit (DNA polymerase delta subunit p125) cfa
CANINE_2:CFAAFFX.5353.1.S1_S_AT similar to DNA polymerase delta catalytic subunit (DNA polymerase delta subunit p125) cfa
CANINE_2:CFAAFFX.5358.1.S1_AT similar to DNA polymerase delta catalytic subunit (DNA polymerase delta subunit p125) cfa
DROSOPHILA_2:1641438_AT DNA-polymerase- dm
DROSGENOME1:143701_AT DNA-polymerase- dm
HG-U95AV2:1462_S_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
HC-G110:1462_S_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
HG-U133A:203422_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
HG-U133_PLUS_2:203422_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
HG-FOCUS:203422_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
HG-U133A_2:203422_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
HU35KSUBA:M80397_S_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
HUGENEFL:M80397_S_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
U133_X3P:G4505932_3P_AT polymerase (DNA directed), delta 1, catalytic subunit 125kDa hs
MOUSE430A_2:1456055_X_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MOE430A:1456055_X_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MOUSE430_2:1456055_X_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MU11KSUBB:Z21848_S_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MG-U74AV2:103057_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MG-U74AV2:161528_R_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MG-U74CV2:165514_F_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MOE430A:1448187_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MOUSE430A_2:1448187_AT polymerase (DNA directed), delta 1, catalytic subunit mm
MOUSE430_2:1448187_AT polymerase (DNA directed), delta 1, catalytic subunit mm
RT-U34:AJ222691CDS_AT polymerase (DNA directed), delta 1, catalytic subunit rn
RG-U34A:AJ222691CDS_AT polymerase (DNA directed), delta 1, catalytic subunit rn
RAE230A:1370127_AT polymerase (DNA directed), delta 1, catalytic subunit rn
RAT230_2:1370127_AT polymerase (DNA directed), delta 1, catalytic subunit rn
YEAST_2:1779349_AT Catalytic subunit of DNA polymerase delta; required for chromosomal DNA replication during mitosis and meiosis, intragenic recombination, repair of double strand DNA breaks, and DNA replication during nucleotide excision repair (NER) Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6260 DNA replication inferred from electronic annotation QuickGO AmiGO
6810 transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
166 nucleotide binding inferred from electronic annotation QuickGO AmiGO
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3887 DNA-directed DNA polymerase activity inferred from electronic annotation QuickGO AmiGO
5215 transporter activity inferred from electronic annotation QuickGO AmiGO
8408 3'-5' exonuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB04077 Hypothetical protein F10C2.4 [Caenorhabditis elegans] ref|NP_506017.1| F10C2.4 [Caenorhabditis elegans] sp|P90829|DPOD_CAEEL DNA polymerase delta catalytic subunit 0.0
blast CAE75373 Hypothetical protein CBG23360 [Caenorhabditis briggsae] 0.0
blast AAF49555 CG5949-PA [Drosophila melanogaster] gb|AAM29531.1| RE60511p [Drosophila melanogaster] ref|NP_524099.2| CG5949-PA [Drosophila melanogaster] sp|P54358|DPOD_DROME DNA polymerase delta catalytic subunit 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006133 EMBL-EBI DNA polymerase B, exonuclease domain 2.5E-79
Pfam IPR006134 EMBL-EBI DNA polymerase B domain 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:191063_AT
gagttccatatgtttttgtcgctgctgcaaaaaatgttccggcatacgaacgagctgaag
atccaacttttgtacttcaaaataacattccattggacaccaaacactacttgactaatc
aactcgccaaaccacttgccagaattttcgagcccatcttgggtgatagagcagaaaaga
ttctggtggaaggagaacatacaagagttcgtacagtcgttcagagtaaagttggaggtc
ttgcagcgttcacaacgaaatctgcaacttgtcttggttgcaagagtgttttaccaagag
cagaatcagagaacgcagtttgcaaacactgtgagccgaagcttccaacgatttttgctt
ctagaatgaacactatgcacgaacttgaaaaccattttggtcgcctctggaccgaatgcc
aaaattgtgcaaagactatgcaagacaaagtgaattgctcggctcgagactgtccgatct
actata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGTTCCATATGTTTTTGTCGCTGC 56 399 2684 Antisense
TTGACTAATCAACTCGCCAAACCAC 114 705 2794 Antisense
CGCCAAACCACTTGCCAGAATTTTC 271 257 2808 Antisense
CCAGAATTTTCGAGCCCATCTTGGG 98 273 2822 Antisense
AAGAGTTCGTACAGTCGTTCAGAGT 117 155 2886 Antisense
AAGTTGGAGGTCTTGCAGCGTTCAC 529 155 2912 Antisense
AACACTGTGAGCCGAAGCTTCCAAC 360 133 3008 Antisense
GCTTCCAACGATTTTTGCTTCTAGA 695 305 3024 Antisense
TGAAAACCATTTTGGTCGCCTCTGG 391 571 3069 Antisense
TCGCCTCTGGACCGAATGCCAAAAT 340 599 3084 Antisense
GCTCGAGACTGTCCGATCTACTATA 589 299 3145 Antisense
Sequence Source Affymetrix Proprietary Database