[Home] | [Total List]

[174287_at] RNA polymerase II elongation factor like

Description C29303_rc /REP_DB=TREMBL Accession /GB=C29303 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk198f3 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 39      6grp_high1_10_10 > 82      4grp_highest_8_8 > 23      4grp_high_8_8 > 06      6grp_highest_nonorm > 57      6grp_total > 80      4grp_total > 02      6grp_highest_sub > 04      6grp_cgc > 96      6grp_high1_sub > 04      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7031
1 2 3 4 range
A 1896.8
(-2.5)
P 		1263.4
(-3)
P 		1492.3
(-2.8)
P 		8294.6
(3)
P 		7031
B 1757.6
(-3)
P 		1990.4
(-2.8)
P 		1893.2
(-2.9)
P 		7494.2
(3)
P 		5737
C 2175.8
(-2.3)
P 		1682.2
(-2.9)
P 		1602.9
(-3)
P 		6224.6
(3)
P 		4622
avr 1943.4
(-2.7) 		1645.3
(-3) 		1662.8
(-3) 		7337.8
(3) 		5693

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1761
1 2 3 4 5 6 range
A 2703.5
(2.2)
P 		1706
(-3)
P 		2411.6
(0.7)
P 		2863.2
(3)
P 		2648.8
(1.9)
P 		2214.5
(-0.4)
P 		1157
B 2768.3
(0.5)
P 		2885.8
(0.9)
P 		1799.8
(-3)
P 		3466.7
(3)
P 		2532
(-0.4)
P 		2447.7
(-0.7)
P 		1667
C 2006.4
(-3)
P 		2301
(-1.7)
P 		2440.8
(-1.1)
P 		3372.6
(3)
P 		2122.3
(-2.5)
P 		2482.4
(-0.9)
P 		1366
avr 2492.7
(-1.4) 		2297.6
(-2.5) 		2217.4
(-3) 		3234.2
(3) 		2434.4
(-1.7) 		2381.5
(-2) 		1017
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1323
1 2 3 4 range
A 690.6
(-0.3)
P 		274.2
(-3)
P 		390.1
(-2.3)
P 		1214.2
(3)
P 		940
B 560.5
(-2.4)
P 		491.6
(-2.7)
P 		438.7
(-3)
P 		1597
(3)
P 		1158
C 720.3
(-0.5)
P 		483.7
(-3)
P 		558.7
(-2.2)
P 		1049.6
(3)
P 		566
avr 657.1
(-1.3) 		416.5
(-3) 		462.5
(-2.7) 		1286.9
(3) 		870

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 592
1 2 3 4 5 6 range
A 498.4
(-3)
P 		606.7
(-0.8)
P 		525.2
(-2.5)
P 		726.2
(1.5)
P 		799.3
(3)
P 		539.2
(-2.2)
P 		301
B 963.2
(2.3)
P 		960.6
(2.3)
P 		437
(-3)
P 		918.2
(1.9)
P 		1028.7
(3)
P 		912.7
(1.8)
P 		592
C 743.7
(0.5)
P 		702.1
(-0.7)
P 		621.2
(-3)
P 		678.2
(-1.4)
P 		686.7
(-1.1)
P 		831
(3)
P 		210
avr 735.1
(1) 		756.5
(1.4) 		527.8
(-3) 		774.2
(1.8) 		838.2
(3) 		761
(1.5) 		310
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174287_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22332
Sequence Type Exemplar sequence
Representative Public ID C29303 NCBI
Target Description C29303_rc /REP_DB=TREMBL Accession /GB=C29303 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk198f3 : 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_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 
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:13223546-13223972(-) 90.61 100.0
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] 2.0E-84
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
Sequence
Target Sequence 
>C. ELEGANS:174287_AT
tcagccaccaccacatttaatgctaatttcccgtgttcaaccgtcttgtattcaatttta
ttttctctgcttcttcgttcaatttatattttaaaactttcgctgtagatttgtaatata
gaaaatttgcctttgatcaacttgactcacaacgccattcacttttcttcaaaaaatttt
acaattccagtttttaatcgtttcattccatctttaataaattcatagtgtattcttcca
gctcttttccacaggtctatgattcgccaaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAGCCACCACCACATTTAATGCTA 647 625 131 Antisense
TAATGCTAATTTCCCGTGTTCAACC 554 635 148 Antisense
CCGTGTTCAACCGTCTTGTATTCAA 486 265 161 Antisense
CTCTGCTTCTTCGTTCAATTTATAT 684 231 195 Antisense
AAAACTTTCGCTGTAGATTTGTAAT 247 129 223 Antisense
AATTTGCCTTTGATCAACTTGACTC 90 175 254 Antisense
TCAACTTGACTCACAACGCCATTCA 73 631 267 Antisense
GTTTTTAATCGTTTCATTCCATCTT 670 447 320 Antisense
TCATAGTGTATTCTTCCAGCTCTTT 368 619 353 Antisense
CAGCTCTTTTCCACAGGTCTATGAT 52 205 369 Antisense
TCCACAGGTCTATGATTCGCCAAAT 197 589 378 Antisense
Sequence Source Affymetrix Proprietary Database