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[192957_s_at] DNA primase 49Kd subunit

Description F58A4.4 /REP_DB=WormBase Gene ID /WP=CE00220 /GEN=pri-1 /TR=SW:P34471 /GB=CAA80161.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=DNA primase 49Kd subunit
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 77      4grp_high_8_8 > 61      6grp_highest_nonorm > 93      6grp_total > 78      4grp_total > 59      6grp_highest_sub > Da      6grp_cgc > 49      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 299
1 2 3 4 range
A 257.8
(0.6)
P 		362.5
(3)
P 		309
(1.7)
P 		106
(-3)
A 		257
B 236.5
(-1.3)
P 		295.4
(0.2)
P 		404.6
(3)
P 		171.6
(-3)
P 		233
C 231.1
(-0.4)
P 		312.2
(1.5)
P 		377.6
(3)
P 		119.3
(-3)
P 		258
avr 241.8
(-0.2) 		323.4
(2) 		363.7
(3) 		132.3
(-3) 		231

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 570
1 2 3 4 5 6 range
A 306.8
(-1.6)
P 		244.4
(-2.6)
P 		241.8
(-2.7)
P 		221.5
(-3)
P 		344.9
(-1)
P 		589.3
(3)
P 		368
B 311.6
(-1.8)
P 		203.9
(-3)
P 		246.5
(-2.5)
P 		281.5
(-2.1)
P 		400.5
(-0.8)
P 		742.8
(3)
P 		539
C 229.9
(-2.4)
P 		234.3
(-2.3)
P 		173.1
(-3)
P 		294.6
(-1.7)
P 		327
(-1.3)
P 		722.9
(3)
P 		550
avr 282.8
(-2.2) 		227.5
(-2.9) 		220.5
(-3) 		265.9
(-2.4) 		357.5
(-1.2) 		685
(3) 		465
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 116
1 2 3 4 range
A 93.9
(3)
P 		78.7
(1.8)
P 		80.8
(2)
P 		15.5
(-3)
A 		78
B 75.4
(1.1)
P 		72.9
(0.8)
P 		93.7
(3)
P 		36.6
(-3)
P 		57
C 76.5
(0)
P 		89.8
(0.8)
P 		131.6
(3)
P 		20.1
(-3)
P 		112
avr 81.9
(1.5) 		80.5
(1.3) 		102
(3) 		24.1
(-3) 		78

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 233
1 2 3 4 5 6 range
A 56.6
(-2.7)
P 		86.9
(-0.7)
P 		52.7
(-3)
P 		56.2
(-2.8)
P 		104.1
(0.4)
P 		143.5
(3)
P 		91
B 108.4
(-1.7)
P 		67.9
(-2.8)
P 		59.9
(-3)
P 		74.6
(-2.6)
P 		162.7
(-0.2)
P 		277
(3)
P 		217
C 85.2
(-1.8)
P 		71.5
(-2.2)
P 		44.1
(-3)
P 		59.2
(-2.5)
P 		105.8
(-1.1)
P 		242
(3)
P 		198
avr 83.4
(-1.9) 		75.4
(-2.2) 		52.2
(-3) 		63.3
(-2.6) 		124.2
(-0.4) 		220.8
(3) 		169
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192957_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6838
Sequence Type Exemplar sequence
Representative Public ID F58A4.4 NCBI
Target Description F58A4.4 /REP_DB=WormBase Gene ID /WP=CE00220 /GEN=pri-1 /TR=SW:P34471 /GB=CAA80161.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=DNA primase 49Kd 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_066725(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066725 NCBI Caenorhabditis elegans DNA PRImase homolog family member (pri-1) (pri-1) mRNA, complete cds. 11/11 None
SNAP00000012193 ENSEMBL cdna:SNAP chromosome:CEL140:III:9612243:9614175:-1 11/11 None
GENEFINDER00000012202 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:9612243:9614175:-1 11/11 None
F58A4.4 ENSEMBL cdna:known chromosome:CEL140:III:9612210:9614177:-1 gene:F58A4.4 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
chrIII:9612238-9614171(-) 100.0 100.0
chrIII:877582-879561(-) 92.21 92.38
Public Domain and Genome References
Gene Title DNA primase 49Kd subunit
Gene Symbol pri-1
Ensembl F58A4.4
Entrez Gene 176358 Entrez gene
SwissProt P34471 EMBL-EBI
WormBase CE00220 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:249276_AT DNA primase small subunit family at
CANINE:1605013_AT similar to DNA primase small subunit (DNA primase 49 kDa subunit) (p49) cfa
CANINE:1587436_AT similar to DNA primase small subunit (DNA primase 49 kDa subunit) (p49) cfa
CANINE_2:CFA.579.1.A1_AT similar to DNA primase small subunit (DNA primase 49 kDa subunit) (p49) cfa
CANINE_2:CFAAFFX.1187.1.S1_AT similar to DNA primase small subunit (DNA primase 49 kDa subunit) (p49) cfa
DROSOPHILA_2:1633854_AT DNA polymerase 50kD dm
DROSGENOME1:143688_AT DNA polymerase 50kD dm
CHICKEN:GGAAFFX.11368.1.S1_AT similar to DNA primase small subunit (DNA primase 49 kDa subunit) (p49) gga
HG-U95AV2:798_AT primase, polypeptide 1, 49kDa hs
HC-G110:798_AT primase, polypeptide 1, 49kDa hs
HG-U133_PLUS_2:205053_AT primase, polypeptide 1, 49kDa hs
HG-U133A:205053_AT primase, polypeptide 1, 49kDa hs
HG-FOCUS:205053_AT primase, polypeptide 1, 49kDa hs
HG-U133A_2:205053_AT primase, polypeptide 1, 49kDa hs
HUGENEFL:X74330_AT primase, polypeptide 1, 49kDa hs
U133_X3P:G4506050_3P_AT primase, polypeptide 1, 49kDa hs
HG-U95AV2:36400_AT Primase, polypeptide 1, 49kDa hs
MU11KSUBA:D13544_S_AT DNA primase, p49 subunit mm
MU11KSUBB:MSA.28335.0_F_AT DNA primase, p49 subunit mm
MG-U74AV2:96772_AT DNA primase, p49 subunit mm
MOE430A:1449061_A_AT DNA primase, p49 subunit mm
MOUSE430A_2:1449061_A_AT DNA primase, p49 subunit mm
MOUSE430_2:1449061_A_AT DNA primase, p49 subunit mm
MOE430A:1418369_AT DNA primase, p49 subunit mm
MOUSE430A_2:1418369_AT DNA primase, p49 subunit mm
MOUSE430_2:1418369_AT DNA primase, p49 subunit mm
MOE430B:1444544_AT DNA primase, p49 subunit (Prim1), mRNA mm
MOUSE430_2:1444544_AT DNA primase, p49 subunit (Prim1), mRNA mm
MU19KSUBC:TC37822_AT DNA primase, p49 subunit (Prim1), mRNA mm
MU19KSUBC:TC37822_G_AT DNA primase, p49 subunit (Prim1), mRNA mm
YEAST_2:1776090_AT Subunit of DNA primase, which is required for DNA synthesis and double-strand break repair Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6269 DNA replication, synthesis of RNA primer inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3896 DNA primase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA80161 Hypothetical protein F58A4.4 [Caenorhabditis elegans] ref|NP_499126.1| DNA PRImase homolog family member (pri-1) [Caenorhabditis elegans] sp|P34471|PRI1_CAEEL DNA primase small subunit 0.0
blast CAE65161 Hypothetical protein CBG10030 [Caenorhabditis briggsae] 0.0
blast AAC68924 Hypothetical protein T24C4.5 [Caenorhabditis elegans] ref|NP_497283.2| T24C4.5 [Caenorhabditis elegans] 1.0E-161
Protein Domains
Database ID Description E-Value
Pfam IPR002755 EMBL-EBI DNA primase, small subunit 1.8E-55
Pfam IPR002755 EMBL-EBI DNA primase, small subunit 4.4E-16
Sequence
Target Sequence 
>C. ELEGANS:192957_S_AT
gaaagttccgccgattgtgcgtgacgcgtttaacgttgcattgaaagatggagttttcga
gaagatgatctatgaccagggatggctggataaggaagattttatcacagagtacaagtt
tatgtcagaagtaggcagagatgacttgcgtagcctttccgagacttacaaaactccaca
agaacgctggaacatgattcgtgggctttttgatgacgactatcgcaaatcgctttctcc
gaaggacggtcttctcgattttaaaatgcaaggtcgcgaccgaaattatcttctctactt
tgttcttcaacgatgctatccacgtcttgatgttaatgtatctacaggaacaaatcactt
gctcaaatccccattctgcattcatccaaagaccggaaacgttgcagttcctctgaatgt
cggtaaaattgaagagttcgatgtaagcaaatgtcctcgaattgatcatgtcgtggaaga
gttgagcagtcttttggctgaacgaggaaacgacgagaacgaggattcgaagaatcgaaa
attcctggcgtacaagcatggagctctcgcaccttacgttgaaaac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAAGTTCCGCCGATTGTGCGTGAC 682 359 627 Antisense
GTGCGTGACGCGTTTAACGTTGCAT 220 479 643 Antisense
AGATGATCTATGACCAGGGATGGCT 97 65 689 Antisense
TAGCCTTTCCGAGACTTACAAAACT 674 607 777 Antisense
GCTGGAACATGATTCGTGGGCTTTT 452 293 812 Antisense
CTATCGCAAATCGCTTTCTCCGAAG 267 225 846 Antisense
TTCTCCGAAGGACGGTCTTCTCGAT 423 693 861 Antisense
CGCGACCGAAATTATCTTCTCTACT 218 255 901 Antisense
TCCCCATTCTGCATTCATCCAAAGA 219 597 994 Antisense
GAGTTGAGCAGTCTTTTGGCTGAAC 131 397 1105 Antisense
AGCTCTCGCACCTTACGTTGAAAAC 79 79 1188 Antisense
Sequence Source Affymetrix Proprietary Database