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[173959_at] RNA polymerase II elongation factor like

Description CEK098D5R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K08H2.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D72393 /WB_GENE_ID=K08H2.1 /WP=CE06159 /CHR=X /FEA=Genomic Cluster /GEN=skr-21 /DEF=RNA polymerase II elongation factor like; C.elegans cDNA clone yk98d5 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 97      6grp_high1_10_10 > 78      4grp_high_8_8 > 37      6grp_highest_nonorm > 81      6grp_total > 59      4grp_total > 42      6grp_highest_sub > Cu      6grp_cgc > 39      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 137
1 2 3 4 range
A 96.6
(-3)
P 		166.9
(3)
P 		155.5
(2)
P 		123.1
(-0.7)
A 		70
B 76.9
(-3)
A 		183.1
(3)
P 		162.1
(1.8)
P 		137
(0.4)
P 		106
C 175.5
(-0.9)
P 		214.3
(3)
P 		154.2
(-3)
P 		193.2
(0.9)
P 		60
avr 116.3
(-3) 		188.1
(3) 		157.3
(0.4) 		151.1
(-0.1) 		72

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 211
1 2 3 4 5 6 range
A 289.4
(1.1)
P 		148.8
(-3)
P 		260
(0.3)
P 		214.9
(-1.1)
P 		225.5
(-0.8)
P 		353.9
(3)
P 		205
B 290.2
(3)
P 		224.6
(-3)
P 		235
(-2)
P 		266.8
(0.9)
P 		252.3
(-0.5)
P 		271.6
(1.3)
P 		66
C 301.3
(1.1)
P 		183.2
(-2.8)
P 		176.5
(-3)
P 		290.9
(0.7)
P 		278.6
(0.3)
P 		359.9
(3)
P 		183
avr 293.6
(1.5) 		185.5
(-3) 		223.8
(-1.4) 		257.5
(0) 		252.1
(-0.2) 		328.5
(3) 		143
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44
1 2 3 4 range
A 35.2
(1.6)
P 		36.2
(1.8)
P 		40.6
(3)
P 		18
(-3)
A 		23
B 24.5
(-3)
A 		45.2
(3)
P 		37.6
(0.8)
P 		29.2
(-1.6)
P 		21
C 58.1
(2.3)
P 		61.6
(3)
P 		53.7
(1.4)
P 		32.6
(-3)
P 		29
avr 39.3
(0.6) 		47.7
(3) 		44
(1.9) 		26.6
(-3) 		21

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 76
1 2 3 4 5 6 range
A 53.4
(-2.9)
P 		52.9
(-3)
P 		56.6
(-2.3)
P 		54.5
(-2.7)
P 		68
(-0.3)
P 		86.2
(3)
P 		33
B 101
(2.8)
P 		74.8
(-0.7)
P 		57.1
(-3)
P 		70.7
(-1.2)
P 		102.5
(3)
P 		101.3
(2.8)
P 		45
C 111.7
(2.3)
P 		55.9
(-2.1)
P 		44.9
(-3)
P 		58.5
(-1.9)
P 		90.2
(0.6)
P 		120.5
(3)
P 		76
avr 88.7
(1.3) 		61.2
(-2) 		52.9
(-3) 		61.2
(-2) 		86.9
(1.1) 		102.7
(3) 		50
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173959_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26087
Sequence Type Exemplar sequence
Representative Public ID CEK098D5R NCBI
Target Description CEK098D5R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K08H2.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D72393 /WB_GENE_ID=K08H2.1 /WP=CE06159 /CHR=X /FEA=Genomic Cluster /GEN=skr-21 /DEF=RNA polymerase II elongation factor like; C.elegans cDNA clone yk98d5 : 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_077793(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077793 NCBI Caenorhabditis elegans SKp1 Related (ubiquitin ligase complex component) family member (skr-21) (skr-21) mRNA, complete cds. 11/11 None
K08H2.1 ENSEMBL cdna:known chromosome:CEL140:X:13225731:13226584:-1 gene:K08H2.1 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
chrX:13225762-13226585(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA polymerase II elongation factor like
Gene Symbol skr-21
Ensembl K08H2.1
Entrez Gene 181447 Entrez gene
SwissProt Q21367 EMBL-EBI
WormBase CE06159 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA94149 Hypothetical protein K08H2.1 [Caenorhabditis elegans] ref|NP_510194.1| SKp1 Related (ubiquitin ligase complex component) family member (skr-21) [Caenorhabditis elegans] 4.0E-74
blast AAL34108 SKR-21 [Caenorhabditis elegans] 7.0E-72
blast CAE61402 Hypothetical protein CBG05261 [Caenorhabditis briggsae] 5.0E-41
Protein Domains
Database ID Description E-Value
Pfam IPR001232 EMBL-EBI SKP1 component 3.1E-34
Pfam IPR001232 EMBL-EBI SKP1 component 7.8E-25
Sequence
Target Sequence 
>C. ELEGANS:173959_AT
gctgcatagtttttgatataccatgtttctgtgcctcctgaacttgactcgaactatgta
attactatgcgatctgaacccgaaactgttgtactaaatcttttcactgccttcctgcct
catctcagccttcatttctaaccaaattctcaatttaacacgttctctcaggctttttga
aaaaaaaatcaatcaatcatttgttgtataatttgtaaattaaaaactataatttgtcat
tttaattcctctaatattttttgtata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTGCATAGTTTTTGATATACCATG 665 295 536 Antisense
CCTCCTGAACTTGACTCGAACTATG 253 267 569 Antisense
TGTAATTACTATGCGATCTGAACCC 178 559 592 Antisense
GATCTGAACCCGAAACTGTTGTACT 523 417 606 Antisense
TGTACTAAATCTTTTCACTGCCTTC 464 559 625 Antisense
CTCAGCCTTCATTTCTAACCAAATT 103 229 659 Antisense
AAATTCTCAATTTAACACGTTCTCT 696 115 679 Antisense
ATTTAACACGTTCTCTCAGGCTTTT 269 15 688 Antisense
ACACGTTCTCTCAGGCTTTTTGAAA 120 109 693 Antisense
ATTTGTCATTTTAATTCCTCTAATA 223 19 767 Antisense
TAATTCCTCTAATATTTTTTGTATA 682 631 778 Antisense
Sequence Source Affymetrix Proprietary Database