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[175520_at] DNA repair protein

Description AU114944_rc /REP_DB=TREMBL Accession /GB=AU114944 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk723h10 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 68      6grp_high1_10_10 > 75      4grp_highest_8_8 > 36      4grp_high_8_8 > 0      6grp_highest_nonorm > 96      6grp_total > 76      4grp_total > 15      6grp_highest_sub > In      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 368
1 2 3 4 range
A 771.7
(3)
P 		436.5
(-3)
P 		601.6
(-0)
P 		678.7
(1.3)
P 		335
B 675.2
(0.1)
P 		561.3
(-2.5)
P 		538.5
(-3)
P 		804.8
(3)
P 		266
C 737.2
(2.2)
P 		626.1
(-3)
P 		753.6
(3)
P 		649
(-1.9)
P 		128
avr 728
(3) 		541.3
(-3) 		631.2
(-0.1) 		710.8
(2.4) 		187

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 647
1 2 3 4 5 6 range
A 612.1
(-3)
P 		824.8
(-1)
P 		650.9
(-2.6)
P 		845.4
(-0.8)
P 		849.3
(-0.8)
P 		1259.3
(3)
P 		647
B 695
(-2.2)
P 		623.5
(-3)
P 		732.7
(-1.7)
P 		876.3
(-0.1)
P 		766.2
(-1.3)
P 		1138.5
(3)
P 		515
C 812
(-0.9)
P 		680.8
(-3)
P 		1022.6
(2.5)
P 		1055.5
(3)
P 		725.6
(-2.3)
P 		958.1
(1.4)
P 		375
avr 706.4
(-3) 		709.7
(-3) 		802.1
(-1.6) 		925.7
(0.2) 		780.4
(-1.9) 		1118.6
(3) 		412
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 186
1 2 3 4 range
A 281
(3)
P 		94.8
(-3)
P 		157.3
(-1)
P 		99.3
(-2.9)
P 		186
B 215.3
(3)
P 		138.6
(-2.1)
P 		124.8
(-3)
P 		171.5
(0.1)
P 		91
C 244
(2.3)
P 		180
(-0.2)
P 		262.7
(3)
P 		109.4
(-3)
P 		153
avr 246.8
(3) 		137.8
(-2.4) 		181.6
(-0.3) 		126.7
(-3) 		120

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 312
1 2 3 4 5 6 range
A 112.8
(-3)
P 		293.3
(2.6)
P 		141.7
(-2.1)
P 		214.4
(0.1)
P 		256.3
(1.4)
P 		306.6
(3)
P 		194
B 241.8
(-1.4)
P 		207.5
(-2.3)
P 		177.9
(-3)
P 		232.1
(-1.7)
P 		311.3
(0.2)
P 		424.5
(3)
P 		247
C 301
(2)
P 		207.7
(-3)
P 		260.3
(-0.2)
P 		212.3
(-2.8)
P 		234.8
(-1.6)
P 		320.7
(3)
P 		113
avr 218.5
(-2) 		236.2
(-1.4) 		193.3
(-3) 		219.6
(-2) 		267.5
(-0.2) 		350.6
(3) 		157
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175520_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20931
Sequence Type Exemplar sequence
Representative Public ID AU114944 NCBI
Target Description AU114944_rc /REP_DB=TREMBL Accession /GB=AU114944 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk723h10 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_065960(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065960 NCBI Caenorhabditis elegans T12A2.8 (T12A2.8) mRNA, complete cds. 11/11 None
T12A2.8.1 ENSEMBL cdna:known chromosome:CEL140:III:6244792:6248173:-1 gene:T12A2.8 11/11 None
T12A2.8.2 ENSEMBL cdna:known chromosome:CEL140:III:6245874:6248097:-1 gene:T12A2.8 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:6245933-6246212(-) 100.0 100.0
Public Domain and Genome References
Gene Title DNA repair protein
Ensembl T12A2.8
Entrez Gene 175885 Entrez gene
SwissProt Q22418 EMBL-EBI
WormBase CE01401 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6281 DNA repair inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4518 nuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC24447 Hypothetical protein T12A2.8 [Caenorhabditis elegans] ref|NP_498361.1| T12A2.8 [Caenorhabditis elegans] 0.0
blast CAE70741 Hypothetical protein CBG17486 [Caenorhabditis briggsae] 1.0E-172
blast XP_860452 PREDICTED: similar to DNA-repair protein complementing XP-G cells (Xeroderma pigmentosum group G complementing protein) (DNA excision repair protein ERCC-5) isoform 2 [Canis familiaris] 3.0E-20
Protein Domains
Database ID Description E-Value
Pfam IPR006086 EMBL-EBI XPG I domain 6.1E-46
Pfam IPR006085 EMBL-EBI XPG N-terminal 5.3E-18
Sequence
Target Sequence 
>C. ELEGANS:175520_AT
gttcatccaaattactcatatttcgaatttaaaaattcataattttaaacccccaattca
cacagtatacatcctctcatttttatccaacatttgtctcacacacattccgaaggatcc
ttccacttttttgtactatttcccactctttttctccaaaaatcccgttgaaaattgaaa
attccccttttgattctcga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTCATCCAAATTACTCATATTTCG 259 445 22 Antisense
TTTAAACCCCCAATTCACACAGTAT 21 673 65 Antisense
ACCCCCAATTCACACAGTATACATC 163 91 70 Antisense
CAGTATACATCCTCTCATTTTTATC 688 205 84 Antisense
CATTTTTATCCAACATTTGTCTCAC 586 215 99 Antisense
CAACATTTGTCTCACACACATTCCG 159 189 109 Antisense
GTCTCACACACATTCCGAAGGATCC 204 469 117 Antisense
CACACACATTCCGAAGGATCCTTCC 197 195 121 Antisense
ACATTCCGAAGGATCCTTCCACTTT 492 103 126 Antisense
GATCCTTCCACTTTTTTGTACTATT 100 417 137 Antisense
TGAAAATTCCCCTTTTGATTCTCGA 605 573 197 Antisense
Sequence Source Affymetrix Proprietary Database