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[193758_at] RNA polymerase II elongation factor like

Description R12H7.3 /REP_DB=WormBase Gene ID /WP=CE03568 /GEN=skr-20 /TR=Q21968 /GB=CAA90635.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=RNA polymerase II elongation factor like
Cluster 6grp_highest_10_10 > 11      6grp_high1_10_10 > 01      4grp_highest_8_8 > 31      4grp_high_8_8 > 05      6grp_highest_nonorm > 61      6grp_total > 08      4grp_total > 03      6grp_cgc > 20      6grp_high1_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1447
1 2 3 4 range
A 495.3
(-1.9)
P 		325.3
(-2.6)
P 		221.6
(-3)
P 		1668.2
(3)
P 		1447
B 472
(-2.2)
P 		280.4
(-3)
P 		305.8
(-2.9)
P 		1661.5
(3)
P 		1381
C 529.9
(-1.8)
P 		324.6
(-3)
P 		323.4
(-3)
P 		1315.1
(3)
P 		992
avr 499.1
(-2) 		310.1
(-2.9) 		283.6
(-3) 		1548.3
(3) 		1265

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 380
1 2 3 4 5 6 range
A 665.8
(3)
P 		405.1
(-1.2)
P 		481.9
(0)
P 		379.7
(-1.7)
P 		344.3
(-2.2)
P 		297.7
(-3)
P 		368
B 522.8
(3)
P 		451.6
(0.8)
P 		447.1
(0.6)
P 		480.5
(1.7)
P 		331
(-3)
P 		351
(-2.4)
P 		192
C 531.6
(3)
P 		429.2
(0.5)
P 		385.6
(-0.6)
P 		439.8
(0.8)
P 		286
(-3)
P 		403
(-0.1)
P 		246
avr 573.4
(3) 		428.6
(-0.4) 		438.2
(-0.2) 		433.3
(-0.3) 		320.4
(-3) 		350.6
(-2.3) 		253
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 296
1 2 3 4 range
A 180.3
(0.9)
P 		70.6
(-2.6)
P 		57.9
(-3)
P 		244.2
(3)
P 		186
B 150.5
(-1.3)
P 		69.2
(-3)
P 		70.9
(-3)
P 		354.1
(3)
P 		285
C 175.4
(0.8)
P 		93.3
(-3)
P 		112.7
(-2.1)
P 		221.7
(3)
P 		128
avr 168.7
(-0.2) 		77.7
(-3) 		80.5
(-2.9) 		273.3
(3) 		196

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 125
1 2 3 4 5 6 range
A 122.7
(1.2)
P 		144.1
(3)
P 		104.9
(-0.3)
P 		96.3
(-1)
P 		103.9
(-0.4)
P 		72.5
(-3)
P 		72
B 181.9
(3)
P 		150.3
(0.4)
P 		108.6
(-3)
P 		127.3
(-1.5)
P 		134.5
(-0.9)
P 		130.9
(-1.2)
P 		73
C 197
(3)
P 		131
(-0.6)
P 		98.1
(-2.5)
P 		88.4
(-3)
P 		92.5
(-2.8)
P 		134.9
(-0.4)
P 		109
avr 167.2
(3) 		141.8
(0.6) 		103.9
(-3) 		104
(-3) 		110.3
(-2.4) 		112.8
(-2.2) 		63
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193758_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17975
Sequence Type Exemplar sequence
Representative Public ID R12H7.3 NCBI
Target Description R12H7.3 /REP_DB=WormBase Gene ID /WP=CE03568 /GEN=skr-20 /TR=Q21968 /GB=CAA90635.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=RNA polymerase II elongation factor like
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_077792(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077792 NCBI Caenorhabditis elegans SKp1 Related (ubiquitin ligase complex component) family member (skr-19) (skr-19) mRNA, complete cds. 11/11 A 
SNAP00000017897 ENSEMBL cdna:SNAP chromosome:CEL140:X:13224161:13224628:-1 11/11 None
GENEFINDER00000017898 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:13224161:13224851:-1 11/11 None
R12H7.3 ENSEMBL cdna:known chromosome:CEL140:X:13223537:13224633:-1 gene:R12H7.3 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:13223872-13224628(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA polymerase II elongation factor like
Gene Symbol skr-19
Ensembl R12H7.3
Entrez Gene 181446 Entrez gene
SwissProt Q21968 EMBL-EBI
WormBase CE03568 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA90635 Hypothetical protein R12H7.3 [Caenorhabditis elegans] ref|NP_510193.3| SKp1 Related (ubiquitin ligase complex component) family member (skr-19) [Caenorhabditis elegans] 1.0E-104
blast AAL34106 SKR-19 [Caenorhabditis elegans] 3.0E-87
blast AAL34106 SKR-19 [Caenorhabditis elegans] 1.0E-86
blast CAA90635 Hypothetical protein R12H7.3 [Caenorhabditis elegans] ref|NP_510193.3| SKp1 Related (ubiquitin ligase complex component) family member (skr-19) [Caenorhabditis elegans] 6.0E-85
blast AAL34106 SKR-19 [Caenorhabditis elegans] 2.0E-84
blast CAA90635 Hypothetical protein R12H7.3 [Caenorhabditis elegans] ref|NP_510193.3| SKp1 Related (ubiquitin ligase complex component) family member (skr-19) [Caenorhabditis elegans] 2.0E-84
blast CAE61401 Hypothetical protein CBG05260 [Caenorhabditis briggsae] 5.0E-53
blast CAE61401 Hypothetical protein CBG05260 [Caenorhabditis briggsae] 1.0E-52
Protein Domains
Database ID Description E-Value
Pfam IPR001232 EMBL-EBI SKP1 component 1.6E-31
Pfam IPR001232 EMBL-EBI SKP1 component 1.8E-27
Pfam IPR001232 EMBL-EBI SKP1 component 6.1E-29
Pfam IPR001232 EMBL-EBI SKP1 component 6.1E-29
Pfam IPR001232 EMBL-EBI SKP1 component 1.8E-27
Sequence
Target Sequence 
>C. ELEGANS:193758_AT
aatactctacaaacttcggtcaacagatgggcagagatttctggcagataggcgaacaat
cggaatgataggacggattgaggacctatttagaaatgctggattagacctgattcctgc
cgatcaactgcagccaattcaactagaaatccctgcgacagtgatgaggaaagtgatcga
gtggtgcgaccatcataagcacgacccgccctacgacgaatctgaaccggaaaccaatga
tattcctgactgggatgcgtcgtttctgatggtgaggcacaacatgctctttgatataat
ccgagccgcgagggattttactgtacctggtctcttcgccatgtgctgccgtgtcgtcgg
acaaaatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATACTCTACAAACTTCGGTCAACA 105 173 33 Antisense
GCTGGATTAGACCTGATTCCTGCCG 697 293 130 Antisense
GCCGATCAACTGCAGCCAATTCAAC 205 285 151 Antisense
ATTCAACTAGAAATCCCTGCGACAG 707 11 169 Antisense
TGCGACCATCATAAGCACGACCCGC 403 579 217 Antisense
GCCCTACGACGAATCTGAACCGGAA 192 281 240 Antisense
GATATTCCTGACTGGGATGCGTCGT 428 427 271 Antisense
GATGCGTCGTTTCTGATGGTGAGGC 350 413 286 Antisense
GGTGAGGCACAACATGCTCTTTGAT 593 499 303 Antisense
GATTTTACTGTACCTGGTCTCTTCG 326 429 346 Antisense
TGCTGCCGTGTCGTCGGACAAAATC 197 583 376 Antisense
Sequence Source Affymetrix Proprietary Database