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[192903_at] Domain present in VPS-27, Hrs and STAM

Description W04G3.4 /REP_DB=WormBase Gene ID /WP=CE03788 /TR=Q23165 /GB=CAA92026.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Domain present in VPS-27, Hrs and STAM
Cluster 6grp_highest_10_10 > 32      6grp_high1_10_10 > 12      6grp_highest_nonorm > 70      6grp_total > 22      4grp_total > 54      6grp_highest_sub > De      6grp_cgc > 61      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 439
1 2 3 4 range
A 515
(3)
P 		217.7
(-1.4)
A 		195.1
(-1.7)
A 		110.5
(-3)
A 		405
B 426.8
(3)
P 		183.8
(-3)
A 		217.8
(-2.2)
A 		189.4
(-2.9)
A 		243
C 319.6
(3)
P 		268
(1.7)
P 		205.1
(0.2)
M 		76.4
(-3)
A 		243
avr 420.5
(3) 		223.2
(-1) 		206
(-1.4) 		125.4
(-3) 		295

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 249
1 2 3 4 5 6 range
A 371.8
(3)
P 		355.7
(2.5)
P 		270.8
(-0.4)
P 		230.5
(-1.7)
P 		208.3
(-2.5)
P 		192.3
(-3)
P 		180
B 399.3
(3)
P 		378.4
(2.5)
P 		320.7
(1.1)
P 		182.1
(-2.2)
P 		203.2
(-1.7)
P 		150.8
(-3)
P 		249
C 254.1
(-0)
P 		320
(2.1)
P 		349.5
(3)
P 		309
(1.7)
P 		280.6
(0.8)
P 		159.9
(-3)
P 		190
avr 341.7
(2.7) 		351.4
(3) 		313.7
(1.8) 		240.5
(-0.6) 		230.7
(-0.9) 		167.7
(-3) 		184
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 175
1 2 3 4 range
A 187.5
(3)
P 		47.3
(-1.9)
A 		51
(-1.8)
A 		16.2
(-3)
A 		171
B 136.1
(3)
P 		45.4
(-2.7)
A 		50.5
(-2.4)
A 		40.4
(-3)
A 		96
C 105.8
(3)
P 		77
(1.1)
P 		71.5
(0.8)
M 		12.9
(-3)
A 		93
avr 143.1
(3) 		56.6
(-1.3) 		57.7
(-1.3) 		23.2
(-3) 		120

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 92
1 2 3 4 5 6 range
A 68.5
(-1.4)
P 		126.5
(3)
P 		59
(-2.1)
P 		58.5
(-2.1)
P 		62.8
(-1.8)
P 		46.8
(-3)
P 		80
B 138.9
(3)
P 		126
(2.1)
P 		77.9
(-1)
P 		48.2
(-3)
P 		82.5
(-0.7)
P 		56.2
(-2.5)
P 		91
C 94.2
(2.5)
P 		97.7
(3)
P 		89
(1.8)
P 		62.1
(-1.8)
P 		90.8
(2.1)
P 		53.5
(-3)
P 		44
avr 100.5
(1.5) 		116.7
(3) 		75.3
(-0.9) 		56.3
(-2.6) 		78.7
(-0.5) 		52.2
(-3) 		65
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192903_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16696
Sequence Type Exemplar sequence
Representative Public ID W04G3.4 NCBI
Target Description W04G3.4 /REP_DB=WormBase Gene ID /WP=CE03788 /TR=Q23165 /GB=CAA92026.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Domain present in VPS-27, Hrs and STAM
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_077452(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077452 NCBI Caenorhabditis elegans AdaPTin or adaptin-related protein family member (apt-9) (apt-9) mRNA, complete cds. 10/11 None
SNAP00000042823 ENSEMBL cdna:SNAP chromosome:CEL140:X:11068688:11071699:1 11/11 None
GENEFINDER00000042836 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11068688:11075698:1 11/11 None
W04G3.4 ENSEMBL cdna:known chromosome:CEL140:X:11068449:11071847:1 gene:W04G3.4 10/11 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
chrX:11068687-11071442(+) 100.0 100.0
Public Domain and Genome References
Gene Title Domain present in VPS-27, Hrs and STAM
Gene Symbol apt-9
Ensembl W04G3.4
Entrez Gene 189194 Entrez gene
SwissProt Q23165 EMBL-EBI
WormBase CE31628 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.17715.1.S1_S_AT similar to ADP-ribosylation factor binding protein GGA1 (Golgi-localized, gamma ear-containing, ARF-binding protein 1) (Gamma-adaptin related protein 1) cfa
CANINE_2:CFAAFFX.3135.1.S1_S_AT similar to ADP-ribosylation factor binding protein GGA1 (Golgi-localized, gamma ear-containing, ARF-binding protein 1) (Gamma-adaptin related protein 1) cfa
DROSOPHILA_2:1625681_AT dm
DROSGENOME1:154943_AT dm
CHICKEN:GGAAFFX.23903.1.S1_S_AT similar to ADP-ribosylation factor binding protein GGA1 (Golgi-localized, gamma ear-containing, ARF-binding protein 1) (Gamma-adaptin related protein 1) gga
HG-U133_PLUS_2:218114_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133A:218114_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133A_2:218114_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HU35KSUBA:RC_AA252759_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HU35KSUBA:HUM_ALU_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HU35KSUBB:HUM_ALU_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HU35KSUBC:HUM_ALU_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HU35KSUBD:HUM_ALU_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HUGENEFL:HUM_ALU_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HC-G110:HUM_ALU_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HU35KSUBD:RC_R71934_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
U133_X3P:G9558728_3P_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
U133_X3P:G9558728_3P_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
U133_X3P:HS2.374714.1.S1_3P_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
U133_X3P:HS.190885.0.A1_3P_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
U133_X3P:218114_3P_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133_PLUS_2:1554670_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133A_2:217560_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133_PLUS_2:217560_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133A:217560_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133A_2:45572_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-FOCUS:45572_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133_PLUS_2:45572_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133A:45572_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U95B:45572_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133A_2:50277_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-FOCUS:50277_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133_PLUS_2:50277_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U133A:50277_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U95B:50277_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
HG-U95E:85716_R_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 hs
MU11KSUBB:MSA.9083.0_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 mm
MG-U74AV2:98445_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 mm
MOE430A:1423834_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 mm
MOUSE430A_2:1423834_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 mm
MOUSE430_2:1423834_S_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 mm
MOE430B:1459863_X_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 mm
MOUSE430_2:1459863_X_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 mm
MU19KSUBB:TC34355_AT Golgi associated, gamma adaptin ear containing, ARF binding protein 1 (Gga1), mRNA mm
MU19KSUBB:TC34355_G_AT Golgi associated, gamma adaptin ear containing, ARF binding protein 1 (Gga1), mRNA mm
RG-U34B:RC_AI029572_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 (predicted) rn
RG-U34C:RC_AI175216_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 (predicted) rn
RAE230A:1374761_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 (predicted) rn
RAT230_2:1374761_AT golgi associated, gamma adaptin ear containing, ARF binding protein 1 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6886 intracellular protein transport inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA92026 Hypothetical protein W04G3.4 [Caenorhabditis elegans] ref|NP_509853.2| AdaPTin or adaptin-related protein family member (apt-9) [Caenorhabditis elegans] 0.0
blast CAE70756 Hypothetical protein CBG17505 [Caenorhabditis briggsae] 0.0
blast CAA92027 Hypothetical protein W04G3.5 [Caenorhabditis elegans] ref|NP_509854.1| W04G3.5 [Caenorhabditis elegans] 0.0
blast NP_766636 golgi associated, gamma adaptin ear containing, ARF binding protein 3 [Mus musculus] dbj|BAC27246.1| unnamed protein product [Mus musculus] sp|Q8BMI3|GGA3_MOUSE ADP-ribosylation factor binding protein GGA3 (Golgi-localized, gamma ear-containing, ARF-binding protein 3) 2.0E-36
Protein Domains
Database ID Description E-Value
scop a.4.5.MarR-like transcriptional regulators All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; MarR-like transcriptional regulators 0.629999995231628
scop a.4.5.MarR-like transcriptional regulators All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; MarR-like transcriptional regulators 0.810000002384186
Pfam IPR002014 EMBL-EBI VHS 2.9E-57
Pfam IPR000836 EMBL-EBI Phosphoribosyltransferase 7.4E-22
Sequence
Target Sequence 
>C. ELEGANS:192903_AT
aacaagcgaagtgcctcctaagaacggattttgtgacccccgtgatttggaaggaagttt
gctaaacaatatgatagagtcggagttcgtcgaagaaccaaagatcgttcccgttcaaca
aatgacgcccgttttgaaccggaacagctcagcaagtcctcgtgctagtggagactcttc
tatatttgaaactgattttctggctgggaaacggctcccagaacctctcaaaccaccgac
attgaatgagttgaaaccaaatacaacaacaattacgctagaagctttagaagttctggt
accaccaatgtccccagaaccaacaagtctgtccccaaaagctatccctgagaaagttgc
actgaacccaaggaatcgcgtacccattgaagtactctacagcaaaggtatgaggattct
tctctactattgccaatcag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACAAGCGAAGTGCCTCCTAAGAAC 413 133 999 Antisense
TTGTGACCCCCGTGATTTGGAAGGA 205 243 1029 Antisense
TTCCCGTTCAACAAATGACGCCCGT 507 697 1106 Antisense
TGACGCCCGTTTTGAACCGGAACAG 192 557 1121 Antisense
AACCGGAACAGCTCAGCAAGTCCTC 612 145 1135 Antisense
GTCCTCGTGCTAGTGGAGACTCTTC 2 477 1154 Antisense
GAAGTTCTGGTACCACCAATGTCCC 470 335 1288 Antisense
CAATGTCCCCAGAACCAACAAGTCT 211 183 1304 Antisense
CAACAAGTCTGTCCCCAAAAGCTAT 200 189 1319 Antisense
TGAACCCAAGGAATCGCGTACCCAT 495 571 1361 Antisense
ATTCTTCTCTACTATTGCCAATCAG 600 11 1414 Antisense
Sequence Source Affymetrix Proprietary Database