[Home] | [Total List]

[190056_at] DNA repair protein

Description F57B10.6 /REP_DB=WormBase Gene ID /WP=CE11308 /TR=O44737 /GB=AAB96723.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=DNA repair protein
Cluster 6grp_highest_10_10 > 58      6grp_high1_10_10 > 75      4grp_highest_8_8 > 30      4grp_high_8_8 > 04      6grp_highest_nonorm > 72      6grp_total > 75      4grp_total > 05      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 280
1 2 3 4 range
A 314.4
(-0.7)
P 		227.6
(-3)
P 		273.8
(-1.8)
P 		452.8
(3)
P 		225
B 313.4
(-0.5)
P 		224.3
(-2.8)
P 		215.7
(-3)
P 		449.1
(3)
P 		233
C 289
(-1.3)
P 		208.5
(-3)
P 		223.6
(-2.7)
P 		488.8
(3)
P 		280
avr 305.6
(-0.9) 		220.1
(-3) 		237.7
(-2.6) 		463.6
(3) 		244

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 300
1 2 3 4 5 6 range
A 329.2
(-2.2)
P 		375.6
(-1.1)
P 		296.2
(-3)
P 		412.9
(-0.2)
P 		420.8
(0)
P 		542.4
(3)
P 		246
B 367.4
(-2.4)
P 		353.6
(-3)
P 		385.2
(-1.5)
P 		440.5
(1)
P 		368.4
(-2.3)
P 		483.6
(3)
P 		130
C 267.6
(-3)
P 		436.8
(0.4)
P 		463.1
(0.9)
P 		567.7
(3)
P 		311.5
(-2.1)
P 		508.6
(1.8)
P 		300
avr 321.4
(-3) 		388.7
(-0.9) 		381.5
(-1.1) 		473.7
(1.8) 		366.9
(-1.6) 		511.5
(3) 		190
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 65
1 2 3 4 range
A 114.5
(3)
P 		49.4
(-3)
P 		71.6
(-1)
P 		66.3
(-1.4)
P 		65
B 99.9
(3)
P 		55.4
(-2.4)
P 		50
(-3)
P 		95.7
(2.5)
P 		50
C 95.7
(3)
P 		60
(-3)
P 		77.9
(0)
P 		82.4
(0.8)
P 		36
avr 103.4
(3) 		54.9
(-3) 		66.5
(-1.6) 		81.5
(0.3) 		49

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 120
1 2 3 4 5 6 range
A 60.7
(-3)
P 		133.6
(3)
P 		64.5
(-2.7)
P 		104.7
(0.6)
P 		127
(2.5)
P 		132.1
(2.9)
P 		73
B 127.8
(-0.6)
P 		117.7
(-1.3)
P 		93.5
(-3)
P 		116.7
(-1.4)
P 		149.7
(0.9)
P 		180.3
(3)
P 		87
C 99.2
(-3)
P 		133.3
(-0.1)
P 		117.9
(-1.4)
P 		114.2
(-1.7)
P 		100.8
(-2.9)
P 		170.3
(3)
P 		71
avr 95.9
(-2.7) 		128.2
(0.2) 		92
(-3) 		111.9
(-1.3) 		125.8
(-0.1) 		160.9
(3) 		69
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190056_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.792
Sequence Type Exemplar sequence
Representative Public ID F57B10.6 NCBI
Target Description F57B10.6 /REP_DB=WormBase Gene ID /WP=CE11308 /TR=O44737 /GB=AAB96723.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=DNA repair protein
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_059490(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059490 NCBI Caenorhabditis elegans F57B10.6 (F57B10.6) mRNA, complete cds. 11/11 None
SNAP00000011830 ENSEMBL cdna:SNAP chromosome:CEL140:I:6563035:6570433:1 11/11 None
GENEFINDER00000011844 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:6563035:6571669:1 11/11 None
F57B10.6 ENSEMBL cdna:known chromosome:CEL140:I:6566834:6570433:1 gene:F57B10.6 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
chrI:6566762-6570362(+) 97.95 100.0
Public Domain and Genome References
Gene Title DNA repair protein
Ensembl F57B10.6
Entrez Gene 186441 Entrez gene
SwissProt O44737 EMBL-EBI
WormBase CE11308 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.9967.1.S1_AT similar to XPG-complementing protein cfa
HG-U95AV2:2064_G_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HC-G110:2064_G_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HG-U95AV2:2063_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HC-G110:2063_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HUGENEFL:X69978_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HG-U133A:202414_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HG-U133_PLUS_2:202414_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HG-FOCUS:202414_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HG-U133A_2:202414_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
U133_X3P:G4503600_3P_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HG-U133_PLUS_2:233415_AT Excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
HG-U133B:233415_AT Excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
U133_X3P:HS.291660.0.S1_3P_AT Excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome)) hs
MU11KSUBA:U40796_S_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 mm
MG-U74AV2:103483_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 mm
MG-U74AV2:161777_F_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 mm
MG-U74CV2:171306_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 mm
MOE430A:1450935_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 mm
MOUSE430A_2:1450935_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 mm
MOUSE430_2:1450935_AT excision repair cross-complementing rodent repair deficiency, complementation group 5 mm
MG-U74BV2:108888_AT Excision repair cross-complementing rodent repair deficiency, complementation group 5 (Ercc5), mRNA mm
MOE430B:1457713_AT Excision repair cross-complementing rodent repair deficiency, complementation group 5 (Ercc5), mRNA mm
MOUSE430_2:1457713_AT Excision repair cross-complementing rodent repair deficiency, complementation group 5 (Ercc5), mRNA mm
RAE230B:1383953_AT excision repair cross-complementing rodent repair deficiency,complementation group 5 rn
RAT230_2:1383953_AT excision repair cross-complementing rodent repair deficiency,complementation group 5 rn
RAE230B:1398057_AT Excision repair cross-complementing rodent repair deficiency,complementation group 5 rn
RAT230_2:1398057_AT Excision repair cross-complementing rodent repair deficiency,complementation group 5 rn
YEAST_2:1770170_AT Single-stranded DNA endonuclease, cleaves single-stranded DNA during nucleotide excision repair to excise damaged DNA; subunit of Nucleotide Excision Repair Factor 3 (NEF3); homolog of human XPG protein Sc
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 AAB96723 Hypothetical protein F57B10.6 [Caenorhabditis elegans] ref|NP_491891.1| F57B10.6 [Caenorhabditis elegans] 0.0
blast CAE67220 Hypothetical protein CBG12657 [Caenorhabditis briggsae] 0.0
blast AAB96724 Trehalase protein 1 [Caenorhabditis elegans] ref|NP_491890.2| TREhalase family member (tre-1) [Caenorhabditis elegans] emb|CAD54510.1| trehalase [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006086 EMBL-EBI XPG I domain 6.5E-30
Pfam IPR006085 EMBL-EBI XPG N-terminal 1.4E-12
Pfam IPR001661 EMBL-EBI Glycoside hydrolase, family 37 4.5E-48
Pfam IPR001661 EMBL-EBI Glycoside hydrolase, family 37 9.6E-75
Pfam IPR006086 EMBL-EBI XPG I domain 6.5E-30
Pfam IPR006085 EMBL-EBI XPG N-terminal 4.4E-28
Pfam IPR000348 EMBL-EBI emp24/gp25L/p24 8.4E-37
Pfam IPR001661 EMBL-EBI Glycoside hydrolase, family 37 2.1E-69
Pfam IPR001661 EMBL-EBI Glycoside hydrolase, family 37 7.3E-72
Pfam IPR006086 EMBL-EBI XPG I domain 6.5E-30
Pfam IPR006085 EMBL-EBI XPG N-terminal 4.4E-28
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000011844 1 1550-1572
Sequence
Target Sequence 
>C. ELEGANS:190056_AT
tgttcttaactgctccggatgataaacgagttgctagtcgaaatgcaatgatgttgagaa
gacatgtaactgaagcaaacgatatggagaatatcaaatgtgtgtgctctaatcaagacg
ctgtgcatgcctaccttcatcccatcgttgattcatcatcagaaaaacttcgatggcgcc
agatgaatattccattgatccgtcgaattcttcatcaacgccttcaatggcctgatcgca
aacagcacaacgaagagcagaattcatttgacgctttcgaaaaatggaataattttctaa
aatccggtggacaaagccaaatgcgattagaccgatttttcgcacagaaattggatagtt
ctctcgaactaaaatggtcgaaaaaaattgtcgaggcgctggacaaaattggacaacgtg
tagcgggaactatgaaaaacaatgaaatgtcaaaagaaaagaaagttgataaacaaatca
agaagagcaaaacagctgtgaaacgtgtaactcgtgccagaggaataggtcgcgggaaag
gaggagcacttcttgtaccagctaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTTCTTAACTGCTCCGGATGATAA 590 561 1880 Antisense
TAATCAAGACGCTGTGCATGCCTAC 484 633 1989 Antisense
TTCATCCCATCGTTGATTCATCATC 261 687 2015 Antisense
CCATTGATCCGTCGAATTCTTCATC 187 269 2071 Antisense
CATCAACGCCTTCAATGGCCTGATC 313 213 2092 Antisense
TGGCCTGATCGCAAACAGCACAACG 276 545 2107 Antisense
GAGCAGAATTCATTTGACGCTTTCG 38 391 2134 Antisense
CGATTAGACCGATTTTTCGCACAGA 137 249 2203 Antisense
GTGAAACGTGTAACTCGTGCCAGAG 138 483 2377 Antisense
GTGCCAGAGGAATAGGTCGCGGGAA 29 477 2393 Antisense
AGGAGCACTTCTTGTACCAGCTAAT 58 55 2421 Antisense
Sequence Source Affymetrix Proprietary Database