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[192220_at] endoplasmic reticular protein

Description F46C5.8 /REP_DB=WormBase Gene ID /WP=CE03349 /TR=SW:P52879 /GB=CAA91047.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=endoplasmic reticular protein
Cluster 6grp_highest_10_10 > 01      6grp_high1_10_10 > 10      4grp_highest_8_8 > 12      4grp_high_8_8 > 39      6grp_highest_nonorm > 56      6grp_total > 32      4grp_total > 33      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1485
1 2 3 4 range
A 2122.4
(-2.5)
P 		2035.3
(-3)
P 		2900.5
(2)
P 		3064.3
(3)
P 		1029
B 1578.9
(-3)
P 		2624.2
(3)
P 		2094.5
(-0)
P 		2427.2
(1.9)
P 		1045
C 2002.1
(-2.4)
P 		2740.5
(3)
P 		2723.8
(2.9)
P 		1914.7
(-3)
P 		826
avr 1901.1
(-3) 		2466.7
(2.1) 		2572.9
(3) 		2468.7
(2.1) 		672

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1171
1 2 3 4 5 6 range
A 2398.8
(2.3)
P 		2213
(0.6)
P 		2189.6
(0.4)
P 		2478.2
(3)
P 		1984.8
(-1.5)
P 		1814.1
(-3)
P 		664
B 2224
(3)
P 		1801.9
(-1.2)
P 		1754.5
(-1.6)
P 		2111.5
(1.9)
P 		1953
(0.3)
P 		1616.8
(-3)
P 		607
C 2359
(1.3)
P 		2036.5
(-0.3)
P 		2689.6
(3)
P 		2378.1
(1.4)
P 		2008.3
(-0.5)
P 		1518.6
(-3)
P 		1171
avr 2327.3
(3) 		2017.1
(0.3) 		2211.2
(2) 		2322.6
(3) 		1982
(-0.1) 		1649.8
(-3) 		678
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 627
1 2 3 4 range
A 772.8
(3)
P 		441.8
(-3)
P 		758.3
(2.7)
P 		448.6
(-2.9)
P 		331
B 503.5
(-2.3)
P 		648.1
(3)
P 		485.3
(-3)
P 		517.2
(-1.8)
P 		163
C 662.8
(0.3)
P 		787.9
(1.5)
P 		949.3
(3)
P 		322.8
(-3)
P 		627
avr 646.4
(1.3) 		625.9
(0.9) 		731
(3) 		429.5
(-3) 		302

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 448
1 2 3 4 5 6 range
A 442.2
(-3)
P 		787.1
(3)
P 		476.8
(-2.4)
P 		628.5
(0.2)
P 		598.9
(-0.3)
P 		441.7
(-3)
P 		345
B 773.8
(2.7)
P 		599.8
(-0.2)
P 		426.1
(-3)
P 		559.3
(-0.8)
P 		793.5
(3)
P 		602.9
(-0.1)
P 		367
C 874.4
(3)
P 		621.4
(-0.8)
P 		684.5
(0.1)
P 		478.2
(-3)
P 		649.9
(-0.4)
P 		508.4
(-2.5)
P 		396
avr 696.8
(3) 		669.4
(2.1) 		529.1
(-2.6) 		555.3
(-1.7) 		680.8
(2.5) 		517.7
(-3) 		179
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192220_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4001
Sequence Type Exemplar sequence
Representative Public ID F46C5.8 NCBI
Target Description F46C5.8 /REP_DB=WormBase Gene ID /WP=CE03349 /TR=SW:P52879 /GB=CAA91047.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=endoplasmic reticular protein
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_063477(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063477 NCBI Caenorhabditis elegans F46C5.8 (F46C5.8) mRNA, complete cds. 11/11 None
SNAP00000022652 ENSEMBL cdna:SNAP chromosome:CEL140:II:8811292:8812178:1 11/11 None
GENEFINDER00000022665 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8811292:8812178:1 11/11 None
F46C5.8 ENSEMBL cdna:known chromosome:CEL140:II:8811288:8812522:1 gene:F46C5.8 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
chrII:8811288-8812175(+) 100.0 100.0
Public Domain and Genome References
Gene Title endoplasmic reticular protein
Ensembl F46C5.8
Entrez Gene 174410 Entrez gene
SwissProt P52879 EMBL-EBI
WormBase CE03349 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:14646_S_AT RER1A protein at
ATH1-121501:252913_AT RER1A protein at
DROSOPHILA_2:1637556_AT dm
DROSGENOME1:150569_AT dm
CHICKEN:GGA.1255.2.S1_S_AT similar to RER1 homolog gga
CHICKEN:GGAAFFX.13212.1.S1_S_AT similar to RER1 homolog gga
MOUSE430_2:1460706_S_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae) mm
MOUSE430A_2:1460706_S_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae) mm
MOE430A:1460706_S_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae) mm
MOUSE430_2:1460660_X_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae) mm
MOUSE430A_2:1460660_X_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae) mm
MOE430A:1460660_X_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae) mm
MG-U74AV2:160518_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae) mm
MU19KSUBA:TC18976_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:35656 IMAGE:4036721) mm
MU19KSUBB:TC31311_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:35656 IMAGE:4036721) mm
MU19KSUBB:TC31311_G_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:35656 IMAGE:4036721) mm
MU11KSUBB:W34451_S_AT RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:35656 IMAGE:4036721) mm
RG-U34C:RC_AI171272_AT similar to RER1 homolog (predicted) rn
RAE230A:1373382_AT similar to RER1 homolog (predicted) rn
RAT230_2:1373382_AT similar to RER1 homolog (predicted) rn
RAE230B:1395596_AT Similar to RER1 homolog (predicted) rn
RAT230_2:1395596_AT Similar to RER1 homolog (predicted) rn
RG-U34C:RC_AI171277_AT Similar to RER1 homolog (predicted) rn
YEAST_2:1777240_AT Protein involved in retention of membrane proteins, including Sec12p, in the ER; localized to Golgi; functions as a retrieval receptor in returning membrane proteins to the ER Sc
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA91047 Hypothetical protein F46C5.8 [Caenorhabditis elegans] ref|NP_495878.1| F46C5.8 [Caenorhabditis elegans] sp|P52879|YAF8_CAEEL Hypothetical protein F46C5.8 in chromosome II 1.0E-109
blast CAE59740 Hypothetical protein CBG03181 [Caenorhabditis briggsae] 1.0E-107
blast XP_609109 PREDICTED: similar to RER1 homolog [Bos taurus] 2.0E-62
Protein Domains
Database ID Description E-Value
Pfam IPR004932 EMBL-EBI Retrieval of early ER protein Rer1 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495878.1 3 35-54,59-81,138-157
F46C5.8 3 35-54,59-81,138-157
SNAP00000022652 3 35-54,59-81,138-157
GENEFINDER00000022665 3 35-54,59-81,138-157
Sequence
Target Sequence 
>C. ELEGANS:192220_AT
gacaggccaggtgtaacatctcgtttctttcacagtttggaagtgaagtatcaatactat
ctcgatcgtctcacgccacatactgcattccgatgggttatcgctctgatctcgctcgtc
ttctttgcgtctagaattattctcttgcaaggattctacattgttgcatatgctgtcggt
atctactatttgaatctcttcttgctctttttaactccatcaattgatccagctttagag
ttcgaggatgaagatgatggtccagttcttccatcgaaaacaaacgacgaattccgccca
ttcatgcgtcgtctgccagagtttaagttttggcactccttcatgaaggccactctgatc
gcaatcacttgcaccttcttcgaattcttcgatgttccagtattctggccaattcttgtc
atgtatttcttcatccttaccttcctcactctcaagagacag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACAGGCCAGGTGTAACATCTCGTT 320 369 31 Antisense
CATCTCGTTTCTTTCACAGTTTGGA 692 211 47 Antisense
TCAATACTATCTCGATCGTCTCACG 408 633 81 Antisense
GCCACATACTGCATTCCGATGGGTT 98 279 105 Antisense
GTTGCATATGCTGTCGGTATCTACT 562 439 193 Antisense
TTCTTGCTCTTTTTAACTCCATCAA 631 689 229 Antisense
CCTTCATGAAGGCCACTCTGATCGC 518 267 368 Antisense
TGATCGCAATCACTTGCACCTTCTT 176 565 386 Antisense
TCCAGTATTCTGGCCAATTCTTGTC 272 591 426 Antisense
TCATGTATTTCTTCATCCTTACCTT 182 623 449 Antisense
TACCTTCCTCACTCTCAAGAGACAG 268 651 468 Antisense
Sequence Source Affymetrix Proprietary Database