[Home] | [Total List]

[174268_s_at]

Description CEC748_rc /REP_DB=TREMBL Accession /GB=C07748 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk158f7 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 77      6grp_high1_10_10 > 87      6grp_highest_nonorm > 92      6grp_total > 78      4grp_total > 14      6grp_highest_sub > Da      6grp_high1_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 218
1 2 3 4 range
A 177.8
(2.2)
P 		75.3
(-2.4)
A 		62.2
(-3)
A 		195.1
(3)
P 		133
B 176.3
(2.9)
P 		133.1
(0.3)
A 		78.1
(-3)
P 		177.2
(3)
P 		99
C 178.9
(-0.1)
P 		81.7
(-3)
A 		115.6
(-2)
P 		280.6
(3)
P 		199
avr 177.7
(1.2) 		96.7
(-2.5) 		85.3
(-3) 		217.6
(3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 629
1 2 3 4 5 6 range
A 148.9
(-2.6)
P 		122.8
(-3)
P 		143.5
(-2.7)
P 		153.3
(-2.5)
P 		303.7
(-0.2)
P 		507.1
(3)
P 		384
B 107
(-3)
P 		188.1
(-2.2)
P 		152.2
(-2.6)
P 		212.3
(-2)
P 		347.5
(-0.6)
P 		720.7
(3)
P 		614
C 116.8
(-3)
P 		127.9
(-2.9)
P 		135.1
(-2.8)
P 		153
(-2.6)
P 		235
(-1.9)
P 		735.6
(3)
P 		619
avr 124.2
(-3) 		146.3
(-2.7) 		143.6
(-2.8) 		172.9
(-2.4) 		295.4
(-1.1) 		654.5
(3) 		530
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 48
1 2 3 4 range
A 64.7
(3)
P 		16.3
(-3)
A 		16.3
(-3)
A 		28.6
(-1.5)
P 		48
B 56.2
(3)
P 		32.9
(-0.7)
A 		18.1
(-3)
P 		37.8
(0.1)
P 		38
C 59.2
(3)
P 		23.5
(-3)
A 		40.3
(-0.2)
P 		47.3
(1)
P 		36
avr 60
(3) 		24.2
(-3) 		24.9
(-2.9) 		37.9
(-0.7) 		36

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 241
1 2 3 4 5 6 range
A 27.5
(-3)
P 		43.7
(-2)
P 		31.3
(-2.8)
P 		38.9
(-2.3)
P 		91.6
(1)
P 		123.5
(3)
P 		96
B 37.2
(-3)
P 		62.6
(-2.3)
P 		37
(-3)
P 		56.2
(-2.5)
P 		141.2
(-0.3)
P 		268.7
(3)
P 		232
C 43.3
(-2.7)
P 		39
(-2.8)
P 		34.4
(-2.9)
P 		30.8
(-3)
P 		76
(-1.7)
P 		246.2
(3)
P 		215
avr 36
(-2.9) 		48.4
(-2.5) 		34.2
(-3) 		42
(-2.7) 		102.9
(-0.7) 		212.8
(3) 		179
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174268_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20214
Sequence Type Exemplar sequence
Representative Public ID CEC748 NCBI
Target Description CEC748_rc /REP_DB=TREMBL Accession /GB=C07748 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk158f7 : 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_059140(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059140 NCBI Caenorhabditis elegans F56A3.2 (F56A3.2) mRNA, complete cds. 11/11 A 
GENEFINDER00000016720 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5182739:5186143:1 11/11 None
SNAP00000016710 ENSEMBL cdna:SNAP chromosome:CEL140:I:5184708:5186143:1 11/11 None
F56A3.2 ENSEMBL cdna:known chromosome:CEL140:I:5182739:5186220:1 gene:F56A3.2 11/11 A 
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:5185661-5186157(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl F56A3.2
Entrez Gene 172157 Entrez gene
SwissProt P91351 EMBL-EBI
WormBase CE11216 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.3226.2.S1_AT similar to GIY-YIG domain containing 2 isoform 1 cfa
CANINE_2:CFAAFFX.26193.1.S1_S_AT similar to GIY-YIG domain containing 2 isoform 1 cfa
DROSOPHILA_2:1632047_AT dm
DROSGENOME1:149286_AT dm
HG-U133_PLUS_2:233334_X_AT GIY-YIG domain containing 2 hs
HG-U133B:233334_X_AT GIY-YIG domain containing 2 hs
HG-U133_PLUS_2:218317_X_AT GIY-YIG domain containing 2 hs
HG-U133A:218317_X_AT GIY-YIG domain containing 2 hs
HG-U133A_2:218317_X_AT GIY-YIG domain containing 2 hs
HU35KSUBD:RC_H97169_AT GIY-YIG domain containing 2 hs
U133_X3P:G13129003_3P_S_AT GIY-YIG domain containing 2 hs
U133_X3P:G13129003_3P_A_AT GIY-YIG domain containing 2 hs
HG-U95C:64454_AT GIY-YIG domain containing 2 hs
HG-U95E:80466_S_AT GIY-YIG domain containing 2 hs
MOUSE430_2:1454082_A_AT GIY-YIG domain containing 2 mm
MOE430A:1454082_A_AT GIY-YIG domain containing 2 mm
MOUSE430A_2:1454082_A_AT GIY-YIG domain containing 2 mm
MG-U74BV2:164625_AT GIY-YIG domain containing 2 (Giyd2), mRNA mm
MU19KSUBA:TC22483_AT GIY-YIG domain containing 2 (Giyd2), mRNA mm
MU19KSUBA:TC22483_G_AT GIY-YIG domain containing 2 (Giyd2), mRNA mm
MU19KSUBB:TC30529_AT GIY-YIG domain containing 2 (Giyd2), mRNA mm
MU19KSUBC:TC39140_AT GIY-YIG domain containing 2 (Giyd2), mRNA mm
RAE230B:1378215_AT similar to RIKEN cDNA 4833422P03 (predicted) rn
RAT230_2:1378215_AT similar to RIKEN cDNA 4833422P03 (predicted) rn
RAE230B:1379654_AT similar to RIKEN cDNA 4833422P03 (predicted) rn
RAT230_2:1379654_AT similar to RIKEN cDNA 4833422P03 (predicted) rn
YEAST_2:1772420_AT Subunit of a complex, with Slx4p, that hydrolyzes 5' branches from duplex DNA in response to stalled or converging replication forks; function overlaps with that of Sgs1p-Top3p Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6281 DNA repair inferred from electronic annotation QuickGO AmiGO
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
4518 nuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB37804 Hypothetical protein F56A3.2 [Caenorhabditis elegans] ref|NP_491541.1| F56A3.2 [Caenorhabditis elegans] 0.0
blast AAB37804 Hypothetical protein F56A3.2 [Caenorhabditis elegans] ref|NP_491541.1| F56A3.2 [Caenorhabditis elegans] 1.0E-134
blast CAE56129 Hypothetical protein CBG23741 [Caenorhabditis briggsae] 1.0E-97
blast CAE56129 Hypothetical protein CBG23741 [Caenorhabditis briggsae] 3.0E-97
blast CAE56129 Hypothetical protein CBG23741 [Caenorhabditis briggsae] 4.0E-95
blast EAL42010 ENSANGP00000026512 [Anopheles gambiae str. PEST] ref|XP_565552.1| ENSANGP00000026512 [Anopheles gambiae str. PEST] 1.0E-37
Protein Domains
Database ID Description E-Value
Pfam IPR000305 EMBL-EBI Excinuclease ABC, C subunit, N-terminal 4.7E-16
Sequence
Target Sequence 
>C. ELEGANS:174268_S_AT
gatgtatttccgcaacttgtccatcacattttcactccaaatgcttgtcggaaaacggtt
tgaaactgaaaaacgaacatgtggaccacgtatacccgctgaaagccaattgcccaacat
gtggacaattttatttatggggagatattatcagagagcaacgacggattatcaagaatg
cgctgaagagttccaaaacatggttgtgcggaaagaactccctcatcgagaaatcagtcc
aat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGTATTTCCGCAACTTGTCCATC 584 409 13 Antisense
GCAACTTGTCCATCACATTTTCACT 613 319 24 Antisense
ATTTTCACTCCAAATGCTTGTCGGA 322 15 40 Antisense
AACATGTGGACCACGTATACCCGCT 603 135 88 Antisense
TATACCCGCTGAAAGCCAATTGCCC 384 657 103 Antisense
AGCCAATTGCCCAACATGTGGACAA 284 83 116 Antisense
CAGAGAGCAACGACGGATTATCAAG 516 205 164 Antisense
AATGCGCTGAAGAGTTCCAAAACAT 317 165 189 Antisense
GAGTTCCAAAACATGGTTGTGCGGA 53 399 200 Antisense
GTTGTGCGGAAAGAACTCCCTCATC 531 433 215 Antisense
TCCCTCATCGAGAAATCAGTCCAAT 475 597 231 Antisense
Sequence Source Affymetrix Proprietary Database