[Home] | [Total List]

[173907_at] WD domain, G-beta repeat (3 domains)

Description CEK038E2R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=R03E1.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D33938 /WB_GENE_ID=R03E1.1 /WP=CE18901 /CHR=X /FEA=Genomic Cluster /DEF=WD domain, G-beta repeat (3 domains); C.elegans cDNA clone yk38e2 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 26      4grp_highest_8_8 > 29      4grp_high_8_8 > 07      6grp_highest_nonorm > 60      6grp_total > 26      4grp_total > 0      6grp_highest_sub > Cu      6grp_cgc > 04      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 205
1 2 3 4 range
A 397.1
(-0.1)
P 		344.8
(-3)
P 		392.6
(-0.4)
P 		453.3
(3)
P 		109
B 347.8
(0)
P 		248.4
(-3)
P 		302.1
(-1.4)
P 		445.9
(3)
P 		198
C 318.4
(-3)
P 		350
(-0.4)
P 		390.1
(3)
P 		344.5
(-0.8)
P 		72
avr 354.4
(-0.6) 		314.4
(-3) 		361.6
(-0.2) 		414.6
(3) 		100

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 418
1 2 3 4 5 6 range
A 647
(3)
P 		447.4
(0)
P 		307.5
(-2)
P 		242.1
(-3)
P 		408.5
(-0.5)
P 		368.7
(-1.1)
P 		405
B 493.7
(2.1)
P 		540.7
(3)
P 		263.3
(-2.3)
P 		229.1
(-3)
P 		309.3
(-1.5)
P 		348.3
(-0.7)
P 		312
C 470.6
(1.5)
P 		537
(3)
P 		268.8
(-3)
P 		315.1
(-2)
P 		302.3
(-2.3)
P 		422.8
(0.4)
P 		268
avr 537.1
(3) 		508.4
(2.4) 		279.9
(-2.6) 		262.1
(-3) 		340
(-1.3) 		379.9
(-0.4) 		275
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 87
1 2 3 4 range
A 144.6
(3)
P 		74.8
(-2.4)
P 		102.6
(-0.2)
P 		66.4
(-3)
P 		78
B 110.9
(3)
P 		61.3
(-3)
P 		70
(-1.9)
P 		95
(1.1)
P 		50
C 105.4
(0.6)
P 		100.6
(0.3)
P 		136
(3)
P 		58.1
(-3)
P 		78
avr 120.3
(3) 		78.9
(-2.3) 		102.9
(0.8) 		73.2
(-3) 		47

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 119
1 2 3 4 5 6 range
A 119.3
(0.6)
P 		159.1
(3)
P 		67
(-2.7)
P 		61.4
(-3)
P 		123.3
(0.8)
P 		89.8
(-1.3)
P 		98
B 171.8
(2.6)
P 		180
(3)
P 		63.9
(-2.8)
P 		60.7
(-3)
P 		125.7
(0.3)
P 		129.9
(0.5)
P 		119
C 174.4
(3)
P 		163.8
(2.4)
P 		68.4
(-2.7)
P 		63.4
(-3)
P 		97.8
(-1.1)
P 		141.5
(1.2)
P 		111
avr 155.2
(2.3) 		167.6
(3) 		66.4
(-2.7) 		61.8
(-3) 		115.6
(0.1) 		120.4
(0.3) 		106
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173907_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26097
Sequence Type Exemplar sequence
Representative Public ID CEK038E2R NCBI
Target Description CEK038E2R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=R03E1.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D33938 /WB_GENE_ID=R03E1.1 /WP=CE18901 /CHR=X /FEA=Genomic Cluster /DEF=WD domain, G-beta repeat (3 domains); C.elegans cDNA clone yk38e2 : 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_077960(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077960 NCBI Caenorhabditis elegans SYnthetic lethal with Mec family member (sym-4) (sym-4) mRNA, complete cds. 11/11 None
R03E1.1.1 ENSEMBL cdna:known chromosome:CEL140:X:14164561:14169619:-1 gene:R03E1.1 11/11 None
R03E1.1.2 ENSEMBL cdna:known chromosome:CEL140:X:14164575:14169539:-1 gene:R03E1.1 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
chrX:14164582-14169517(-) 99.15 100.0
Public Domain and Genome References
Gene Title WD domain, G-beta repeat (3 domains)
Gene Symbol sym-4
Ensembl R03E1.1
Entrez Gene 181527 Entrez gene
SwissProt Q9XTZ0 EMBL-EBI
WormBase CE18901 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:248198_AT WD-40 repeat family protein at
CANINE:1604698_AT similar to WD repeat domain 44 protein cfa
CANINE_2:CFAAFFX.28001.1.S1_S_AT similar to WD repeat domain 44 protein cfa
DROSOPHILA_2:1641708_AT dm
DROSGENOME1:152769_AT dm
CHICKEN:GGA.16521.1.S1_S_AT WD repeat domain 44 gga
CHICKEN:GGAAFFX.11748.1.S1_S_AT WD repeat domain 44 gga
HG-U95E:67602_AT WD repeat domain 44 hs
HU35KSUBD:RC_AA426299_AT WD repeat domain 44 hs
HG-U133A:219297_AT WD repeat domain 44 hs
HG-U133_PLUS_2:219297_AT WD repeat domain 44 hs
HG-FOCUS:219297_AT WD repeat domain 44 hs
HG-U133A_2:219297_AT WD repeat domain 44 hs
U133_X3P:G9506636_3P_AT WD repeat domain 44 hs
HG-U95B:56033_AT WD repeat domain 44 hs
HG-U133_PLUS_2:235485_AT WD repeat domain 44 hs
HG-U133B:235485_AT WD repeat domain 44 hs
HG-U133_PLUS_2:240789_AT WD repeat domain 44 hs
HG-U133B:240789_AT WD repeat domain 44 hs
HG-U95C:63134_R_AT WD repeat domain 44 hs
U133_X3P:HS.186850.0.A1_3P_AT WD repeat domain 44 hs
HU35KSUBB:RC_W80619_AT WD repeat domain 44 hs
U133_X3P:HS.269636.0.A1_3P_AT WD repeat domain 44 hs
MG-U74CV2:168387_I_AT WD repeat domain 44 mm
MOE430B:1430775_AT WD repeat domain 44 mm
MOUSE430_2:1430775_AT WD repeat domain 44 mm
MOE430B:1435051_AT WD repeat domain 44 mm
MOUSE430_2:1435051_AT WD repeat domain 44 mm
RAE230B:1397843_AT WD repeat domain 44 rn
RAT230_2:1397843_AT WD repeat domain 44 rn
RAE230B:1393955_AT WD repeat domain 44 rn
RAT230_2:1393955_AT WD repeat domain 44 rn
Protein Similarities
Method ID Description E-Value
blast AAQ75758 SYM-4 [Caenorhabditis elegans] emb|CAB07400.1| Hypothetical protein R03E1.1 [Caenorhabditis elegans] ref|NP_510361.1| SYnthetic lethal with Mec family member (sym-4) [Caenorhabditis elegans] 0.0
blast CAE69932 Hypothetical protein CBG16308 [Caenorhabditis briggsae] 0.0
blast XP_392050 PREDICTED: similar to CG7814-PA [Apis mellifera] 1.0E-123
Protein Domains
Database ID Description E-Value
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 2.3E-6
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 1.4E-9
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 4.1E-8
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.61
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 2.3E-5
Sequence
Target Sequence 
>C. ELEGANS:173907_AT
actctgcttacctagttttcttaataacagatattaatcatttttctttgaaaatttata
actttcctccgttttactaccaacggcgtcaaaccgaccccgagtgagctttattagcaa
attccactagatttttgtttttttttaatcaaaccgcacgatgtcaatagttaatttttg
aatttttgaatctttgaattttcatcccactctactctttttagccctattggtctccaa
attctatgatgatgtcttttgtttttttgctcgcgcagctttgcttttctctaggaataa
cctatgtgatgtgtaaacctttcgtcctaaacgggatatgaatttcttttcttctgggat
aatttctgca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACTCTGCTTACCTAGTTTTCTTAAT 534 99 3131 Antisense
CGACCCCGAGTGAGCTTTATTAGCA 128 251 3225 Antisense
GTGAGCTTTATTAGCAAATTCCACT 403 483 3234 Antisense
ATCAAACCGCACGATGTCAATAGTT 202 27 3278 Antisense
CTCTACTCTTTTTAGCCCTATTGGT 200 231 3340 Antisense
TTTTTAGCCCTATTGGTCTCCAAAT 456 673 3348 Antisense
GGTCTCCAAATTCTATGATGATGTC 422 503 3362 Antisense
TTTGCTTTTCTCTAGGAATAACCTA 256 659 3410 Antisense
GTGATGTGTAAACCTTTCGTCCTAA 294 483 3436 Antisense
GGGATATGAATTTCTTTTCTTCTGG 497 495 3463 Antisense
CTTTTCTTCTGGGATAATTTCTGCA 238 223 3476 Antisense
Sequence Source Affymetrix Proprietary Database