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[175459_at] RAS-related protein

Description AV181564_rc /REP_DB=TREMBL Accession /GB=AV181564 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk622a3 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 92      6grp_high1_10_10 > 39      4grp_highest_8_8 > 33      4grp_high_8_8 > 50      6grp_highest_nonorm > 67      6grp_total > 19      4grp_total > 61      6grp_highest_sub > Cu      6grp_cgc > 01      6grp_high1_sub > Cu      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 850
1 2 3 4 range
A 2396.4
(3)
P 		2261.8
(2)
P 		2136.8
(1.2)
P 		1546.6
(-3)
P 		850
B 2243.5
(3)
P 		1832
(-2.7)
P 		1997.9
(-0.4)
P 		1807.4
(-3)
P 		436
C 1979.4
(0.9)
P 		2105.1
(3)
P 		2025.4
(1.6)
P 		1752.2
(-3)
P 		353
avr 2206.4
(3) 		2066.3
(1.3) 		2053.4
(1.2) 		1702.1
(-3) 		504

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1478
1 2 3 4 5 6 range
A 2595.3
(3)
P 		2070.2
(-0.5)
P 		1800.8
(-2.3)
P 		1693.7
(-3)
P 		2221.4
(0.5)
P 		2120.4
(-0.2)
P 		902
B 2319.7
(3)
P 		1538.4
(-0.9)
P 		1117
(-3)
P 		2058.1
(1.7)
P 		1911.8
(1)
P 		2287.4
(2.8)
P 		1203
C 1991.2
(2.8)
P 		1714.2
(0.3)
P 		1973.2
(2.6)
P 		2018.6
(3)
P 		1839.6
(1.4)
P 		1350.8
(-3)
P 		668
avr 2302.1
(3) 		1774.3
(-1.7) 		1630.3
(-3) 		1923.5
(-0.4) 		1990.9
(0.2) 		1919.5
(-0.4) 		672
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 646
1 2 3 4 range
A 872.5
(3)
P 		491
(-0.5)
P 		558.6
(0.1)
P 		226.4
(-3)
P 		646
B 715.4
(3)
P 		452.4
(-1.8)
P 		463
(-1.6)
P 		385.2
(-3)
P 		330
C 655.2
(2.3)
P 		605.2
(1.5)
P 		705.9
(3)
P 		295.5
(-3)
P 		410
avr 747.7
(3) 		516.2
(-0.1) 		575.8
(0.7) 		302.4
(-3) 		445

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 582
1 2 3 4 5 6 range
A 478.4
(-1.5)
P 		736.2
(3)
P 		392.2
(-3)
P 		429.6
(-2.3)
P 		670.3
(1.9)
P 		516.3
(-0.8)
P 		344
B 807.1
(2.5)
P 		512.1
(-0.5)
P 		271.2
(-3)
P 		545.1
(-0.2)
P 		776.7
(2.2)
P 		852.9
(3)
P 		582
C 738
(3)
P 		523
(-0.9)
P 		502.2
(-1.3)
P 		405.9
(-3)
P 		595.3
(0.4)
P 		452.2
(-2.2)
P 		332
avr 674.5
(2.9) 		590.4
(1.1) 		388.5
(-3) 		460.2
(-1.5) 		680.8
(3) 		607.1
(1.5) 		292
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175459_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20175
Sequence Type Exemplar sequence
Representative Public ID AV181564 NCBI
Target Description AV181564_rc /REP_DB=TREMBL Accession /GB=AV181564 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk622a3 : 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_060080(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060080 NCBI Caenorhabditis elegans RAB family member (rab-5) (rab-5) mRNA, complete cds. 11/11 None
F26H9.6.1 ENSEMBL cdna:known chromosome:CEL140:I:9316560:9318344:1 gene:F26H9.6 11/11 None
F26H9.6.2 ENSEMBL cdna:known chromosome:CEL140:I:9316565:9318334:1 gene:F26H9.6 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
chrI:9317921-9318204(+) 100.0 100.0
Public Domain and Genome References
Gene Title RAS-related protein
Gene Symbol rab-5
Ensembl F26H9.6
Entrez Gene 172755 Entrez gene
SwissProt P91857 EMBL-EBI
WormBase CE09711 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:17952_AT Ras-related protein (RHA1) / small GTP-binding protein at
ATH1-121501:248983_AT Ras-related protein (RHA1) / small GTP-binding protein at
CANINE:1582669_AT RAB5A, member RAS oncogene family cfa
CANINE_2:CFA.3879.1.S1_S_AT RAB5A, member RAS oncogene family cfa
CANINE_2:CFA.634.1.S1_AT RAB5A, member RAS oncogene family cfa
CHICKEN:GGAAFFX.12840.1.S1_S_AT RAB5A, member RAS oncogene family gga
HG-U133_PLUS_2:206113_S_AT RAB5A, member RAS oncogene family hs
HG-U133A:206113_S_AT RAB5A, member RAS oncogene family hs
HG-U133A_2:206113_S_AT RAB5A, member RAS oncogene family hs
HG-U95AV2:600_AT RAB5A, member RAS oncogene family hs
HC-G110:600_AT RAB5A, member RAS oncogene family hs
HG-U133A:209089_AT RAB5A, member RAS oncogene family hs
HG-U133_PLUS_2:209089_AT RAB5A, member RAS oncogene family hs
HG-FOCUS:209089_AT RAB5A, member RAS oncogene family hs
HG-U133A_2:209089_AT RAB5A, member RAS oncogene family hs
HG-U95AV2:36110_AT RAB5A, member RAS oncogene family hs
HUGENEFL:M28215_AT RAB5A, member RAS oncogene family hs
U133_X3P:G4759003_3P_A_AT RAB5A, member RAS oncogene family hs
U133_X3P:G12654846_3P_AT RAB5A, member RAS oncogene family hs
U133_X3P:HS.296683.0.S1_3P_AT RAB5A, member RAS oncogene family hs
HG-U133A_2:215956_AT RAB5A, member RAS oncogene family hs
HG-U133_PLUS_2:215956_AT RAB5A, member RAS oncogene family hs
HG-U133A:215956_AT RAB5A, member RAS oncogene family hs
HG-U133A_2:215958_AT RAB5A, member RAS oncogene family hs
HG-U133_PLUS_2:215958_AT RAB5A, member RAS oncogene family hs
HG-U133A:215958_AT RAB5A, member RAS oncogene family hs
HG-U95E:72198_AT RAB5A, member RAS oncogene family hs
MU11KSUBB:MSA.23303.0_S_AT RAB5A, member RAS oncogene family mm
MG-U74AV2:94478_AT RAB5A, member RAS oncogene family mm
MOE430A:1416426_AT RAB5A, member RAS oncogene family mm
MOUSE430A_2:1416426_AT RAB5A, member RAS oncogene family mm
MOUSE430_2:1416426_AT RAB5A, member RAS oncogene family mm
MU19KSUBB:TC27886_I_AT RAB5A, member RAS oncogene family, mRNA (cDNA clone MGC:18688 IMAGE:3709729) mm
MU19KSUBC:TC40316_AT RAB5A, member RAS oncogene family, mRNA (cDNA clone MGC:18688 IMAGE:3709729) mm
RG-U34A:AF072935_AT RAB5A, member RAS oncogene family rn
RAE230A:1388800_AT RAB5A, member RAS oncogene family rn
RAT230_2:1388800_AT RAB5A, member RAS oncogene family rn
RAE230A:1387641_AT RAB5A, member RAS oncogene family rn
RAT230_2:1387641_AT RAB5A, member RAS oncogene family rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6886 intracellular protein transport inferred from electronic annotation QuickGO AmiGO
7264 small GTPase mediated signal transduction inferred from electronic annotation QuickGO AmiGO
15031 protein transport inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5525 GTP binding inferred from electronic annotation QuickGO AmiGO
3924 GTPase activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB04205 Hypothetical protein F26H9.6 [Caenorhabditis elegans] ref|NP_492481.1| RAB family member (rab-5) [Caenorhabditis elegans] 1.0E-107
blast CAG32396 hypothetical protein [Gallus gallus] ref|NP_001006363.1| RAB5A, member RAS oncogene family [Gallus gallus] 2.0E-81
blast NP_073183 RAB5A, member RAS oncogene family [Rattus norvegicus] gb|AAC26004.1| small GTP-binding protein rab5 [Rattus norvegicus] 9.0E-81
Protein Domains
Database ID Description E-Value
Pfam IPR001806 EMBL-EBI Ras GTPase superfamily 4.6E-97
Sequence
Target Sequence 
>C. ELEGANS:175459_AT
tttgaacaagttttttgtgctcgctttctttatttattttcactcttttaacccatattt
tctcattttttgtatatttctgactaatgttcagccagtgaatgagcttgcacaattggc
tctgcccatttgctttttatatgcgaaaactcccattttttcattcaaatgttccaatta
tttattgcttctcaccatcaacatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTTGAACAAGTTTTTTGTGCTCGCT 416 665 36 Antisense
TTTTGTGCTCGCTTTCTTTATTTAT 287 679 48 Antisense
TATTTTCACTCTTTTAACCCATATT 199 663 70 Antisense
TATTTCTGACTAATGTTCAGCCAGT 68 663 110 Antisense
GTTCAGCCAGTGAATGAGCTTGCAC 267 445 124 Antisense
TGAGCTTGCACAATTGGCTCTGCCC 105 569 138 Antisense
ACAATTGGCTCTGCCCATTTGCTTT 485 115 147 Antisense
TGCTTTTTATATGCGAAAACTCCCA 693 563 166 Antisense
GCGAAAACTCCCATTTTTTCATTCA 238 289 178 Antisense
AATTATTTATTGCTTCTCACCATCA 462 175 211 Antisense
TTTATTGCTTCTCACCATCAACATC 191 675 216 Antisense
Sequence Source Affymetrix Proprietary Database