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[191933_at] DNA polymerase alpha subunit

Description Y47D3A.29 /REP_DB=WormBase Gene ID /WP=CE26106 /TR=Q9NAH1 /GB=CAB97239.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=DNA polymerase alpha subunit
Cluster 6grp_high1_10_10 > 69      4grp_high_8_8 > 62      6grp_total > 59      4grp_total > 56      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 114
1 2 3 4 range
A 134.3
(-1.9)
P 		120
(-3)
P 		198.7
(3)
P 		127.7
(-2.4)
M 		79
B 142.5
(0.3)
P 		153.1
(0.9)
P 		187.9
(3)
P 		86.7
(-3)
P 		101
C 147.9
(-0.1)
P 		169.5
(1.2)
P 		200.9
(3)
P 		98.4
(-3)
A 		103
avr 141.6
(-0.6) 		147.5
(-0.2) 		195.8
(3) 		104.3
(-3) 		92

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 246
1 2 3 4 5 6 range
A 137.5
(-1.2)
P 		161
(-0.6)
P 		70
(-3)
P 		136.6
(-1.2)
P 		169
(-0.4)
P 		294.9
(3)
P 		225
B 102.7
(-1.3)
P 		76.7
(-2.1)
M 		48.6
(-3)
P 		108.8
(-1.1)
P 		119.9
(-0.8)
P 		239.9
(3)
P 		191
C 202.7
(3)
P 		95.2
(-2.4)
P 		82.6
(-3)
P 		137.9
(-0.2)
A 		199.1
(2.8)
P 		186.1
(2.2)
P 		120
avr 147.6
(-0.2) 		111
(-1.5) 		67.1
(-3) 		127.8
(-0.9) 		162.7
(0.3) 		240.3
(3) 		173
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 53
1 2 3 4 range
A 48.9
(2.5)
P 		26.1
(-1.7)
P 		51.9
(3)
P 		18.7
(-3)
M 		33
B 45.4
(3)
P 		37.8
(1.3)
P 		43.5
(2.6)
P 		18.5
(-3)
P 		27
C 49
(0.6)
P 		48.7
(0.6)
P 		70
(3)
P 		16.6
(-3)
A 		53
avr 47.8
(1.8) 		37.5
(0.2) 		55.1
(3) 		17.9
(-3) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 78
1 2 3 4 5 6 range
A 25.4
(-1.9)
P 		57.2
(1.5)
P 		15.2
(-3)
P 		34.6
(-0.9)
P 		51
(0.8)
P 		71.8
(3)
P 		57
B 35.8
(-1.1)
P 		25.5
(-1.9)
M 		11.8
(-3)
P 		28.8
(-1.7)
P 		48.7
(-0.2)
P 		89.5
(3)
P 		78
C 75.1
(3)
P 		29
(-2.1)
P 		21
(-3)
P 		27.7
(-2.3)
A 		64.4
(1.8)
P 		62.3
(1.6)
P 		54
avr 45.4
(0) 		37.2
(-0.8) 		16
(-3) 		30.4
(-1.5) 		54.7
(1) 		74.5
(3) 		59
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191933_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7966
Sequence Type Exemplar sequence
Representative Public ID Y47D3A.29 NCBI
Target Description Y47D3A.29 /REP_DB=WormBase Gene ID /WP=CE26106 /TR=Q9NAH1 /GB=CAB97239.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=DNA polymerase alpha subunit
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_067036(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067036 NCBI Caenorhabditis elegans Y47D3A.29 (Y47D3A.29) mRNA, complete cds. 11/11 None
SNAP00000007205 ENSEMBL cdna:SNAP chromosome:CEL140:III:11142325:11168625:1 11/11 None
Y47D3A.29 ENSEMBL cdna:known chromosome:CEL140:III:11142325:11154028:1 gene:Y47D3A.29 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000007297 2/11 Cross Hyb Matching Probes None
GENEFINDER00000007263 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:11142320-11153817(+) 100.0 100.0
Public Domain and Genome References
Gene Title DNA polymerase alpha subunit
Ensembl Y47D3A.29
Entrez Gene 176544 Entrez gene
SwissProt Q9NAH1 EMBL-EBI
WormBase CE32262 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247028_AT DNA-directed DNA polymerase alpha catalytic subunit, putative at
CANINE:1586372_AT similar to DNA polymerase alpha catalytic subunit cfa
CANINE_2:CFA.5876.1.A1_AT similar to DNA polymerase alpha catalytic subunit cfa
CANINE_2:CFAAFFX.20910.1.S1_S_AT similar to DNA polymerase alpha catalytic subunit cfa
DROSOPHILA_2:1633249_AT DNA polymerase 180kD dm
DROSGENOME1:153301_AT DNA polymerase 180kD dm
CHICKEN:GGA.12097.1.S1_S_AT polymerase (DNA directed), alpha gga
CHICKEN:GGAAFFX.24932.3.S1_S_AT polymerase (DNA directed), alpha gga
HG-U95AV2:786_AT polymerase (DNA directed), alpha hs
HC-G110:786_AT polymerase (DNA directed), alpha hs
HG-U133_PLUS_2:204835_AT polymerase (DNA directed), alpha hs
HG-U133A_2:204835_AT polymerase (DNA directed), alpha hs
HG-U133A:204835_AT polymerase (DNA directed), alpha hs
HG-FOCUS:204835_AT polymerase (DNA directed), alpha hs
HUGENEFL:X06745_AT polymerase (DNA directed), alpha hs
U133_X3P:G8393994_3P_AT polymerase (DNA directed), alpha hs
U133_X3P:HS2.269556.1.S1_3P_S_AT Polymerase (DNA directed), alpha hs
HG-U133_PLUS_2:1557809_A_AT Polymerase (DNA directed), alpha hs
HG-U95D:88200_AT Polymerase (DNA directed), alpha hs
MU11KSUBA:D17384_S_AT polymerase (DNA directed), alpha 1 mm
MG-U74AV2:103207_AT polymerase (DNA directed), alpha 1 mm
MOE430A:1419397_AT polymerase (DNA directed), alpha 1 mm
MOUSE430A_2:1419397_AT polymerase (DNA directed), alpha 1 mm
MOUSE430_2:1419397_AT polymerase (DNA directed), alpha 1 mm
MOUSE430_2:1456285_AT Polymerase (DNA directed), alpha 1 (Pola1), mRNA mm
MOE430B:1456285_AT Polymerase (DNA directed), alpha 1 (Pola1), mRNA mm
MOE430B:1459319_AT Polymerase (DNA directed), alpha 1 (Pola1), mRNA mm
MOUSE430_2:1459319_AT Polymerase (DNA directed), alpha 1 (Pola1), mRNA mm
MU19KSUBA:TC17880_S_AT Polymerase (DNA directed), alpha 1 (Pola1), mRNA mm
YEAST_2:1776526_AT Catalytic subunit of the DNA polymerase alpha-primase complex, required for the initiation of DNA replication during mitotic DNA synthesis and premeiotic DNA synthesis Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6260 DNA replication inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus 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
8408 3'-5' exonuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB97239 Hypothetical protein Y47D3A.29 [Caenorhabditis elegans] ref|NP_499437.2| Y47D3A.29 [Caenorhabditis elegans] 0.0
blast CAE67630 Hypothetical protein CBG13184 [Caenorhabditis briggsae] 0.0
blast BAD92009.1 DNA polymerase alpha catalytic subunit [Iguana iguana] 0.0
blast CAB55094 Hypothetical protein Y47D3A.4 [Caenorhabditis elegans] ref|NP_499438.1| Caenorhabditis KU family member (cku-70) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006164 EMBL-EBI Ku 1.4E-66
Pfam IPR005161 EMBL-EBI Ku70/Ku80 N-terminal alpha/beta domain 1.7E-76
Pfam IPR006133 EMBL-EBI DNA polymerase B, exonuclease domain 7.8E-17
Pfam IPR006134 EMBL-EBI DNA polymerase B domain 1.0E-126
Pfam IPR005160 EMBL-EBI Ku70/Ku80 C-terminal arm 1.9E-29
Sequence
Target Sequence 
>C. ELEGANS:191933_AT
gaattcatgtgatttgtccactcgatgggtgcggtcattcaaatgtgattcgagagacat
ttgattgtgtgactgatgcctcgtctccccgccttctattctccggatgtgctcaatgtc
aaggatcatgggatcttcaggagcatcaagcagtgattgggaatcaagttgaccgacaaa
tgtcggaattcgtcgccagacatcatctcgcagcgtttaaatgcgatgagccaacgtgtg
aattcaaaactcgcgtacaaacgatgaaatggtgtcgagaaggactcgaatgtattcgat
gctcaactggtgtgctccgtcgtgaatacacttcaaaacagcttttcgatcagcaaatgt
tctttcgaacaattctcgatgtcgacgcggctgtacgaaagttgagcgacgcccaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAATTCATGTGATTTGTCCACTCGA 347 325 3731 Antisense
TCCACTCGATGGGTGCGGTCATTCA 416 589 3747 Antisense
TGATTGTGTGACTGATGCCTCGTCT 497 563 3792 Antisense
TATTCTCCGGATGTGCTCAATGTCA 559 663 3827 Antisense
GGATCATGGGATCTTCAGGAGCATC 699 511 3853 Antisense
ACAAATGTCGGAATTCGTCGCCAGA 393 111 3906 Antisense
CAGACATCATCTCGCAGCGTTTAAA 573 205 3927 Antisense
ATTCGATGCTCAACTGGTGTGCTCC 613 9 4024 Antisense
TGTGCTCCGTCGTGAATACACTTCA 460 555 4041 Antisense
TCGATGTCGACGCGGCTGTACGAAA 367 599 4106 Antisense
GTACGAAAGTTGAGCGACGCCCAGA 30 453 4123 Antisense
Sequence Source Affymetrix Proprietary Database