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[188693_at] Ras family

Description Y11D7A.4 /REP_DB=WormBase Gene ID /WP=CE19030 /TR=Q9XWR6 /GB=CAA21582.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Ras family
Cluster 6grp_high1_10_10 > 07      4grp_high_8_8 > 18      6grp_total > 06      4grp_total > 29      6grp_cgc > 10      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 310
1 2 3 4 range
A 323.4
(2.4)
P 		241.3
(0.7)
P 		69.5
(-3)
A 		350.6
(3)
P 		281
B 379.8
(3)
P 		203.1
(-0.5)
P 		80.9
(-3)
A 		221.3
(-0.2)
P 		299
C 332.4
(3)
P 		195.7
(-0.4)
P 		93.6
(-3)
P 		293.8
(2)
P 		239
avr 345.2
(3) 		213.4
(0) 		81.3
(-3) 		288.6
(1.7) 		264

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 279
1 2 3 4 5 6 range
A 324.3
(3)
P 		168.1
(-1.2)
P 		202.1
(-0.3)
P 		164.8
(-1.3)
P 		158.6
(-1.4)
P 		99.6
(-3)
A 		225
B 378.5
(3)
P 		216.7
(-0.8)
P 		199.3
(-1.2)
P 		172.1
(-1.9)
P 		160.2
(-2.2)
P 		125.5
(-3)
P 		253
C 271.1
(3)
P 		215.1
(0.8)
P 		174.5
(-0.8)
P 		199.1
(0.2)
P 		123
(-2.8)
P 		118
(-3)
P 		153
avr 324.6
(3) 		200
(-0.6) 		192
(-0.8) 		178.7
(-1.2) 		147.3
(-2.1) 		114.4
(-3) 		210
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 103
1 2 3 4 range
A 117.7
(3)
P 		52.4
(-0.9)
P 		18.2
(-3)
A 		51.3
(-1)
P 		100
B 121.1
(3)
P 		50.2
(-1.2)
P 		18.8
(-3)
A 		47.2
(-1.3)
P 		102
C 110
(3)
P 		56.3
(-1.2)
P 		32.6
(-3)
P 		49.5
(-1.7)
P 		77
avr 116.3
(3) 		53
(-1.1) 		23.2
(-3) 		49.3
(-1.3) 		93

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 108
1 2 3 4 5 6 range
A 59.8
(3)
P 		59.8
(3)
P 		44
(0.3)
P 		41.8
(-0)
P 		47.9
(1)
P 		24.2
(-3)
A 		36
B 131.7
(3)
P 		72.1
(-1.2)
P 		48.4
(-2.8)
P 		45.6
(-3)
P 		65.1
(-1.6)
P 		46.8
(-2.9)
P 		86
C 100.5
(3)
P 		65.6
(-0.4)
P 		44.4
(-2.5)
P 		40
(-3)
P 		39.8
(-3)
P 		39.5
(-3)
P 		61
avr 97.3
(3) 		65.8
(-0.1) 		45.6
(-2.1) 		42.5
(-2.4) 		50.9
(-1.6) 		36.8
(-3) 		61
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188693_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9235
Sequence Type Exemplar sequence
Representative Public ID Y11D7A.4 NCBI
Target Description Y11D7A.4 /REP_DB=WormBase Gene ID /WP=CE19030 /TR=Q9XWR6 /GB=CAA21582.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Ras family
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_069208(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069208 NCBI Caenorhabditis elegans RAB family member (rab-28) (rab-28) mRNA, complete cds. 11/11 None
SNAP00000011202 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9242203:9243977:-1 11/11 None
GENEFINDER00000011220 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9242203:9243977:-1 11/11 None
Y11D7A.4 ENSEMBL cdna:known chromosome:CEL140:IV:9242203:9243977:-1 gene:Y11D7A.4 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
chrIV:9242208-9243983(-) 100.0 100.0
Public Domain and Genome References
Gene Title Ras family
Gene Symbol rab-28
Ensembl Y11D7A.4
Entrez Gene 189429 Entrez gene
SwissProt Q9XWR6 EMBL-EBI
WormBase CE19030 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1599715_AT similar to RAB28, member RAS oncogene family isoform 2 cfa
CANINE_2:CFA.1614.1.A1_AT similar to RAB28, member RAS oncogene family isoform 2 cfa
CANINE_2:CFA.19783.1.S1_S_AT similar to RAB28, member RAS oncogene family isoform 2 cfa
CHICKEN:GGA.12657.1.S1_AT RAB28, member RAS oncogene family gga
HG-U133_PLUS_2:207495_AT RAB28, member RAS oncogene family hs
HG-U133A:207495_AT RAB28, member RAS oncogene family hs
HG-FOCUS:207495_AT RAB28, member RAS oncogene family hs
HG-U133A_2:207495_AT RAB28, member RAS oncogene family hs
HU35KSUBA:X94703_AT RAB28, member RAS oncogene family hs
HUGENEFL:X94703_AT RAB28, member RAS oncogene family hs
HU35KSUBC:RC_R54480_AT RAB28, member RAS oncogene family hs
U133_X3P:G4758993_3P_X_AT RAB28, member RAS oncogene family hs
U133_X3P:G4758993_3P_AT RAB28, member RAS oncogene family hs
U133_X3P:HS.166563.1.S1_3P_AT RAB28, member RAS oncogene family hs
U133_X3P:HS.166563.0.S1_3P_A_AT RAB28, member RAS oncogene family hs
U133_X3P:209084_3P_S_AT RAB28, member RAS oncogene family hs
HG-U133A_2:209084_S_AT RAB28, member RAS oncogene family hs
HG-U133_PLUS_2:209084_S_AT RAB28, member RAS oncogene family hs
HG-U133A:209084_S_AT RAB28, member RAS oncogene family hs
HG-U133_PLUS_2:227003_AT RAB28, member RAS oncogene family hs
HG-U133B:227003_AT RAB28, member RAS oncogene family hs
HG-U95AV2:35053_AT RAB28, member RAS oncogene family hs
HG-U95B:44794_S_AT RAB28, member RAS oncogene family hs
HG-U95C:52156_AT RAB28, member RAS oncogene family hs
HG-U133_PLUS_2:234628_AT RAB28, member RAS oncogene family hs
HG-U133B:234628_AT RAB28, member RAS oncogene family hs
U133_X3P:HS.306899.0.S1_3P_AT RAB28, member RAS oncogene family hs
U133_X3P:HS.274556.0.S1_3P_S_AT RAB28, member RAS oncogene family hs
U133_X3P:HS.274556.0.S1_3P_AT RAB28, member RAS oncogene family hs
HG-U133_PLUS_2:233097_X_AT RAB28, member RAS oncogene family hs
HG-U133B:233097_X_AT RAB28, member RAS oncogene family hs
HG-U133_PLUS_2:234674_AT RAB28, member RAS oncogene family hs
HG-U133B:234674_AT RAB28, member RAS oncogene family hs
MOUSE430_2:1453406_A_AT RAB28, member RAS oncogene family mm
MOE430A:1453406_A_AT RAB28, member RAS oncogene family mm
MOUSE430A_2:1453406_A_AT RAB28, member RAS oncogene family mm
MU11KSUBB:MSA.18946.0_S_AT RAB28, member RAS oncogene family mm
MG-U74AV2:99493_AT RAB28, member RAS oncogene family mm
MG-U74CV2:167495_S_AT RAB28, member RAS oncogene family mm
MOE430A:1423990_AT RAB28, member RAS oncogene family mm
MOUSE430A_2:1423990_AT RAB28, member RAS oncogene family mm
MOUSE430_2:1423990_AT RAB28, member RAS oncogene family mm
MU19KSUBB:TC26965_AT RAB28, member RAS oncogene family, mRNA (cDNA clone MGC:8039 IMAGE:3587008) mm
MU19KSUBB:TC26965_G_AT RAB28, member RAS oncogene family, mRNA (cDNA clone MGC:8039 IMAGE:3587008) mm
MU19KSUBC:TC38769_AT RAB28, member RAS oncogene family, mRNA (cDNA clone MGC:8039 IMAGE:3587008) mm
RN-U34:RC_AA893673_S_AT RAB28, member RAS oncogene family rn
RG-U34A:RC_AA893673_S_AT RAB28, member RAS oncogene family rn
RN-U34:X78606_AT RAB28, member RAS oncogene family rn
RG-U34A:X78606_AT RAB28, member RAS oncogene family rn
RAE230A:1368216_AT RAB28, member RAS oncogene family rn
RAT230_2:1368216_AT RAB28, 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
Protein Similarities
Method ID Description E-Value
blast CAA21582 Hypothetical protein Y11D7A.4 [Caenorhabditis elegans] ref|NP_501609.1| RAB family member (rab-28) [Caenorhabditis elegans] 1.0E-117
blast CAE69062 Hypothetical protein CBG15075 [Caenorhabditis briggsae] 4.0E-85
blast AAH45389 RAB28, member RAS oncogene family [Danio rerio] ref|NP_956046.1| RAB28, member RAS oncogene family [Danio rerio] 5.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR001806 EMBL-EBI Ras GTPase superfamily 6.8E-33
Sequence
Target Sequence 
>C. ELEGANS:188693_AT
ctcttggtttggatttcttctctcgtcgaatcacgcttccacacgaaatgcaggtgctcg
tgcaggtatgggatattggaggacaaagtattgctggtgaaatgatcgataagtacttga
ctggagccaacatcgtttttctcgtttatgatgtcaccaactcaaaatcctttgaaaatg
ctgtcgattggttgtcagttgtcaagaaaaacacgaaatccagtgaaacaccggtgaaac
tagtattgatgggaaataagacggatcttgaggagcgacgtgtggtttcagttgaagcac
acaagaattttgcgacttccaacgacatgatgccaacttacgtttctgcaaaaactggag
atactgtatttctcacattcagacaagccgttgctgaagtactcaatgtgggtctttcga
gagctgaagttgaagctgacatcgaaattgttcaaggatctgttattgaacagcctaagc
aatcagacgcctcatatgctcgccgttcggatcaaagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCTTGGTTTGGATTTCTTCTCTCG 178 229 212 Antisense
TCGAATCACGCTTCCACACGAAATG 253 601 237 Antisense
GCAGGTGCTCGTGCAGGTATGGGAT 80 311 261 Antisense
GACTGGAGCCAACATCGTTTTTCTC 460 373 330 Antisense
CGTTTTTCTCGTTTATGATGTCACC 508 247 345 Antisense
AGGAGCGACGTGTGGTTTCAGTTGA 253 55 482 Antisense
GAATTTTGCGACTTCCAACGACATG 92 325 516 Antisense
ACATGATGCCAACTTACGTTTCTGC 532 105 536 Antisense
GATACTGTATTTCTCACATTCAGAC 121 425 571 Antisense
GCAATCAGACGCCTCATATGCTCGC 414 319 690 Antisense
ATATGCTCGCCGTTCGGATCAAAGT 231 21 705 Antisense
Sequence Source Affymetrix Proprietary Database