[Home] | [Total List]

[178267_at]

Description T28D6.9 /REP_DB=WormBase Gene ID /WP=CE24023 /TR=Q9U357 /GB=CAB54316.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 97      6grp_high1_10_10 > 79      4grp_highest_8_8 > 06      4grp_high_8_8 > 22      6grp_highest_nonorm > 92      6grp_total > 89      4grp_total > 17      6grp_highest_sub > Cu      6grp_cgc > 59      6grp_high1_sub > Cu      6grp_cgc_sub > Da      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 261
1 2 3 4 range
A 200.6
(-3)
P 		296.2
(-0.8)
P 		271.4
(-1.4)
P 		461.4
(3)
P 		261
B 260.7
(-3)
P 		270.2
(-2.6)
P 		289.2
(-1.8)
P 		407.8
(3)
P 		147
C 206.8
(-3)
P 		303.5
(-0.4)
P 		309
(-0.2)
P 		429.2
(3)
P 		222
avr 222.7
(-3) 		290
(-1.1) 		289.9
(-1.1) 		432.8
(3) 		210

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 291
1 2 3 4 5 6 range
A 373.7
(3)
P 		176.5
(-3)
P 		305.4
(0.9)
P 		273.6
(-0)
P 		300.4
(0.8)
P 		303.2
(0.9)
P 		197
B 231.3
(-2.4)
P 		276.3
(-1.3)
P 		377.5
(1.1)
P 		208.9
(-3)
P 		345.6
(0.4)
P 		452.7
(3)
P 		244
C 290.2
(-1.1)
P 		297.8
(-1)
P 		214
(-2.9)
P 		210.8
(-3)
P 		366.5
(0.6)
P 		467.5
(3)
P 		257
avr 298.4
(-0.7) 		250.2
(-2.4) 		299
(-0.7) 		231.1
(-3) 		337.5
(0.6) 		407.8
(3) 		177
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 73
(3)
P 		64.3
(-3)
P 		70.9
(1.6)
P 		67.5
(-0.8)
P 		9
B 83.1
(1.9)
P 		66.7
(-3)
P 		67
(-2.9)
P 		86.9
(3)
P 		20
C 68.5
(-3)
P 		87.3
(-0.1)
P 		107.7
(3)
P 		72.4
(-2.4)
P 		39
avr 74.9
(-1.6) 		72.8
(-3) 		81.9
(3) 		75.6
(-1.2) 		9

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 126
1 2 3 4 5 6 range
A 68.9
(-1.7)
P 		62.8
(-3)
P 		66.5
(-2.2)
P 		69.4
(-1.6)
P 		90.7
(3)
P 		73.8
(-0.6)
P 		28
B 80.5
(-1.7)
P 		92
(-1.1)
P 		91.7
(-1.1)
P 		55.3
(-3)
P 		140.4
(1.5)
P 		168.8
(3)
P 		114
C 107.6
(0.4)
P 		90.9
(-0.4)
P 		54.5
(-2.4)
P 		42.4
(-3)
P 		118.6
(1)
P 		156.5
(3)
P 		114
avr 85.7
(-0.7) 		81.9
(-1) 		70.9
(-1.8) 		55.7
(-3) 		116.6
(1.7) 		133
(3) 		77
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 178267_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6388
Sequence Type Exemplar sequence
Representative Public ID T28D6.9 NCBI
Target Description T28D6.9 /REP_DB=WormBase Gene ID /WP=CE24023 /TR=Q9U357 /GB=CAB54316.1 /SUBMIT=HINXTON /CHR=3 /FEA=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_067058(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067058 NCBI Caenorhabditis elegans Presenilin ENhancer (enhancer of sel-12(null)) family member (pen-2) (pen-2) mRNA, complete cds. 11/11 None
SNAP00000023470 ENSEMBL cdna:SNAP chromosome:CEL140:III:11343231:11343879:1 11/11 None
GENEFINDER00000023482 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:11343231:11343879:1 11/11 None
T28D6.9 ENSEMBL cdna:known chromosome:CEL140:III:11343231:11343964:1 gene:T28D6.9 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
chrIII:11343226-11343875(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol pen-2
Ensembl T28D6.9
Entrez Gene 176565 Entrez gene
SwissProt Q9U357 EMBL-EBI
WormBase CE24023 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1603916_X_AT similar to presenilin enhancer 2 cfa
CANINE:1583378_S_AT similar to presenilin enhancer 2 cfa
CANINE_2:CFA.4666.1.A1_AT similar to presenilin enhancer 2 cfa
CANINE_2:CFA.4666.1.A1_S_AT similar to presenilin enhancer 2 cfa
CANINE_2:CFA.6307.1.A1_S_AT similar to presenilin enhancer 2 cfa
CANINE_2:CFA.6307.1.A1_X_AT similar to presenilin enhancer 2 cfa
DROSOPHILA_2:1637469_AT presenilin enhancer dm
HG-U95AV2:35993_S_AT presenilin enhancer 2 homolog (C. elegans) hs
HG-U133_PLUS_2:218302_AT presenilin enhancer 2 homolog (C. elegans) hs
HG-U133A:218302_AT presenilin enhancer 2 homolog (C. elegans) hs
HG-U133A_2:218302_AT presenilin enhancer 2 homolog (C. elegans) hs
HU35KSUBC:RC_N93495_AT presenilin enhancer 2 homolog (C. elegans) hs
U133_X3P:G8923937_3P_X_AT presenilin enhancer 2 homolog (C. elegans) hs
U133_X3P:G8923937_3P_AT presenilin enhancer 2 homolog (C. elegans) hs
U133_X3P:HS.42514.0.S1_3P_A_AT presenilin enhancer 2 homolog (C. elegans) hs
HG-U133A_2:213526_S_AT presenilin enhancer 2 homolog (C. elegans) hs
HG-U133_PLUS_2:213526_S_AT presenilin enhancer 2 homolog (C. elegans) hs
HG-U133A:213526_S_AT presenilin enhancer 2 homolog (C. elegans) hs
HG-U95B:46950_AT presenilin enhancer 2 homolog (C. elegans) hs
HG-U95C:64441_AT presenilin enhancer 2 homolog (C. elegans) hs
HU35KSUBC:RC_AA234185_AT Presenilin enhancer 2 homolog (C. elegans) hs
MU11KSUBB:W40719_S_AT presenilin enhancer 2 homolog (C. elegans) mm
MG-U74AV2:94249_AT presenilin enhancer 2 homolog (C. elegans) mm
MG-U74BV2:164897_F_AT presenilin enhancer 2 homolog (C. elegans) mm
MG-U74CV2:170890_F_AT presenilin enhancer 2 homolog (C. elegans) mm
MOE430A:1415679_AT presenilin enhancer 2 homolog (C. elegans) mm
MOE430B:1415679_AT presenilin enhancer 2 homolog (C. elegans) mm
MOUSE430A_2:1415679_AT presenilin enhancer 2 homolog (C. elegans) mm
MOUSE430_2:1415679_AT presenilin enhancer 2 homolog (C. elegans) mm
MU19KSUBB:TC26235_AT Presenilin enhancer 2 homolog (C. elegans), mRNA (cDNA clone MGC:35751 IMAGE:4984284) mm
MU19KSUBB:TC26235_G_AT Presenilin enhancer 2 homolog (C. elegans), mRNA (cDNA clone MGC:35751 IMAGE:4984284) mm
RG-U34C:RC_AI232272_AT similar to RIKEN cDNA 1700023M09 (predicted) rn
RAE230A:1371338_AT similar to RIKEN cDNA 1700023M09 (predicted) rn
RAT230_2:1371338_AT similar to RIKEN cDNA 1700023M09 (predicted) rn
Protein Similarities
Method ID Description E-Value
blast CAB54316 Hypothetical protein T28D6.9 [Caenorhabditis elegans] ref|NP_499459.1| Presenilin ENhancer (enhancer of sel-12(null)) family member (pen-2) [Caenorhabditis elegans] sp|Q9U357|PEN2_CAEEL Gamma-secretase subunit pen-2 (Presenilin enhancer protein 2) 2.0E-55
blast CAE67641 Hypothetical protein CBG13200 [Caenorhabditis briggsae] 2.0E-51
blast AAO41356 CG33198-PA [Drosophila melanogaster] ref|NP_788401.2| CG33198-PA [Drosophila melanogaster] sp|Q86BE9|PEN2_DROME Gamma-secretase subunit pen-2 (Presenilin enhancer protein 2) 3.0E-23
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499459.1 2 20-39,56-78
T28D6.9 2 20-39,56-78
SNAP00000023470 2 20-39,56-78
GENEFINDER00000023482 2 20-39,56-78
Sequence
Target Sequence 
>C. ELEGANS:178267_AT
ggatatttcaaagctaaccgacgtgaaaaaagttgatttatgtaaaaagtatttcctgat
cggcgcgtgttttctgccgctcgtatggattgtcaacacattttggtttttttccgacgc
gttttgcaaaccgatcaacgcacatcgacgacagattcggaaatacgtgatcgccagcat
tgttggctcgattttctggattattgtgctcagcgcctgggaaatctttttccagcacta
ccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATATTTCAAAGCTAACCGACGTG 237 509 15 Antisense
AAAAAGTATTTCCTGATCGGCGCGT 571 129 58 Antisense
TTTCTGCCGCTCGTATGGATTGTCA 16 671 85 Antisense
TTCCGACGCGTTTTGCAAACCGATC 534 575 126 Antisense
GCAAACCGATCAACGCACATCGACG 280 317 140 Antisense
AACGCACATCGACGACAGATTCGGA 542 145 151 Antisense
GAAATACGTGATCGCCAGCATTGTT 529 363 174 Antisense
AGCATTGTTGGCTCGATTTTCTGGA 579 77 190 Antisense
TCTGGATTATTGTGCTCAGCGCCTG 456 607 209 Antisense
GCTCAGCGCCTGGGAAATCTTTTTC 78 301 222 Antisense
GGGAAATCTTTTTCCAGCACTACCG 216 493 233 Antisense
Sequence Source Affymetrix Proprietary Database