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[190778_at] Human CLN3 protein like

Description F07B10.1 /REP_DB=WormBase Gene ID /WP=CE09198 /TR=Q93440 /GB=CAB01140.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Human CLN3 protein like
Cluster 6grp_high1_10_10 > 23      4grp_highest_8_8 > 42      4grp_high_8_8 > 40      6grp_total > 03      4grp_total > 55      6grp_cgc > 51      6grp_high1_sub > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 379
1 2 3 4 range
A 427.9
(3)
P 		188.9
(-1.8)
P 		215.9
(-1.3)
P 		131.2
(-3)
P 		297
B 445.2
(3)
P 		183.2
(-1.3)
P 		217.2
(-0.7)
P 		78.1
(-3)
P 		367
C 457.2
(3)
P 		188.5
(-2.4)
P 		224.1
(-1.7)
P 		158.4
(-3)
P 		299
avr 443.4
(3) 		186.9
(-1.8) 		219.1
(-1.2) 		122.6
(-3) 		321

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 158
1 2 3 4 5 6 range
A 168
(3)
P 		166.8
(2.9)
P 		157.8
(2.5)
P 		122.2
(0.8)
P 		154.5
(2.4)
P 		41.3
(-3)
A 		127
B 137.8
(0.2)
P 		196
(3)
P 		132.4
(-0.1)
P 		155
(1)
P 		124.9
(-0.5)
P 		72.5
(-3)
P 		124
C 153.6
(1.2)
P 		199.6
(3)
P 		116
(-0.2)
P 		142.6
(0.8)
P 		117.6
(-0.2)
P 		44.3
(-3)
A 		155
avr 153.1
(1.5) 		187.5
(3) 		135.4
(0.7) 		139.9
(0.9) 		132.3
(0.5) 		52.7
(-3) 		135
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 139
1 2 3 4 range
A 155.8
(3)
P 		41
(-2)
P 		56.4
(-1.4)
P 		19.2
(-3)
P 		137
B 142
(3)
P 		45.2
(-1.6)
P 		50.3
(-1.4)
P 		16.6
(-3)
P 		125
C 151.4
(3)
P 		54.2
(-1.7)
P 		78.1
(-0.5)
P 		26.7
(-3)
P 		125
avr 149.7
(3) 		46.8
(-1.8) 		61.6
(-1.1) 		20.8
(-3) 		129

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 55
1 2 3 4 5 6 range
A 31
(-0.5)
P 		59.3
(3)
P 		34.4
(-0)
P 		31
(-0.5)
P 		46.6
(1.5)
P 		10.1
(-3)
A 		49
B 47.9
(0.3)
P 		65.2
(3)
P 		32.2
(-2.2)
P 		41
(-0.8)
P 		50.8
(0.7)
P 		27
(-3)
P 		38
C 56.9
(2.5)
P 		60.9
(3)
P 		29.5
(-1.1)
P 		28.7
(-1.2)
P 		38
(0)
P 		14.8
(-3)
A 		46
avr 45.3
(0.8) 		61.8
(3) 		32
(-1) 		33.6
(-0.8) 		45.1
(0.7) 		17.3
(-3) 		45
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190778_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14012
Sequence Type Exemplar sequence
Representative Public ID F07B10.1 NCBI
Target Description F07B10.1 /REP_DB=WormBase Gene ID /WP=CE09198 /TR=Q93440 /GB=CAB01140.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Human CLN3 protein like
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_073458(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073458 NCBI Caenorhabditis elegans human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.1) (cln-3.1) mRNA, complete cds. 11/11 None
SNAP00000021743 ENSEMBL cdna:SNAP chromosome:CEL140:V:11266185:11268202:-1 11/11 None
GENEFINDER00000021752 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11266185:11268202:-1 11/11 None
F07B10.1 ENSEMBL cdna:known chromosome:CEL140:V:11266185:11268202:-1 gene:F07B10.1 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
chrV:11266184-11268202(-) 100.0 100.0
Public Domain and Genome References
Gene Title Human CLN3 protein like
Gene Symbol cln-3.1
Ensembl F07B10.1
Entrez Gene 179559 Entrez gene
SwissProt Q93440 EMBL-EBI
WormBase CE09198 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1587989_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) cfa
CANINE_2:CFA.14017.1.S1_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) cfa
CANINE_2:CFAAFFX.26221.1.S1_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) cfa
CANINE_2:CFAAFFX.26221.1.S1_S_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) cfa
DROSOPHILA_2:1639653_AT dm
DROSGENOME1:148976_AT dm
HG-U133_PLUS_2:210859_X_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HG-U133A:210859_X_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HG-U133A_2:210859_X_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HG-U95AV2:497_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HC-G110:497_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HU35KSUBD:RC_T47969_S_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HUGENEFL:U32680_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HG-U133A:209275_S_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HG-U133_PLUS_2:209275_S_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HG-FOCUS:209275_S_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
HG-U133A_2:209275_S_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
U133_X3P:G4102728_3P_S_AT ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) hs
MG-U74AV2:102659_AT ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) mm
MU11KSUBA:U68064_S_AT ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) mm
MG-U74AV2:161643_I_AT ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) mm
MOE430A:1417551_AT ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) mm
MOUSE430A_2:1417551_AT ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) mm
MOUSE430_2:1417551_AT ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) mm
MOE430B:1457789_AT ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) mm
MOUSE430_2:1457789_AT ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) mm
MU19KSUBB:TC28975_I_AT Ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) (Cln3), mRNA mm
MU19KSUBB:TC28975_R_AT Ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) (Cln3), mRNA mm
MU19KSUBB:TC28975_S_AT Ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) (Cln3), mRNA mm
MU19KSUBB:TC30633_AT Ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) (Cln3), mRNA mm
MU19KSUBB:TC30633_G_AT Ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) (Cln3), mRNA mm
RG-U34B:RC_AA996529_AT Cln3p rn
RG-U34C:RC_AI180172_AT Cln3p rn
RAE230B:1378479_AT Cln3p rn
RAT230_2:1378479_AT Cln3p rn
RAE230B:1384337_X_AT Cln3p rn
RAT230_2:1384337_X_AT Cln3p rn
RAE230B:1384336_AT Cln3p rn
RAT230_2:1384336_AT Cln3p rn
YEAST_2:1779079_AT Vacuolar membrane protein involved in the ATP-dependent transport of arginine into the vacuole and possibly in balancing ion homeostasis; homolog of human CLN3 involved in Batten disease (juvenile onset neuronal ceroid lipofuscinosis) Sc
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB01140 Hypothetical protein F07B10.1 [Caenorhabditis elegans] ref|NP_505859.1| human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.1) [Caenorhabditis elegans] gb|AAK38269.1| CLN-3.1 [Caenorhabditis elegans] 0.0
blast CAE75206 Hypothetical protein CBG23153 [Caenorhabditis briggsae] 0.0
blast AAC26960 Human cln (neuronal ceroid lipofuscinosis) related protein 3.3 [Caenorhabditis elegans] ref|NP_505237.1| human CLN (neuronal ceroid lipofuscinosis) related family member (cln-3.3) [Caenorhabditis elegans] gb|AAK38268.1| CLN-3.3 [Caenorhabditis elegans] 1.0E-133
Protein Domains
Database ID Description E-Value
Pfam IPR003492 EMBL-EBI Battens disease protein Cln3 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505859.1 8 12-31,92-111,116-138,148-170,183-205,324-346,353-375,395-417
F07B10.1 8 12-31,92-111,116-138,148-170,183-205,324-346,353-375,395-417
SNAP00000021743 8 12-31,92-111,116-138,148-170,183-205,324-346,353-375,395-417
GENEFINDER00000021752 8 12-31,92-111,116-138,148-170,183-205,324-346,353-375,395-417
Sequence
Target Sequence 
>C. ELEGANS:190778_AT
ttgaggctgctgaagcccggggagatgttctaaataccaaaaaagttccacaacgggagc
ttggaccgctcgaacgaattaaactaattggtccactgttgtatctgatggttccacttg
caactgtatacactgctgaatatatgattaatcaaggattgactgaacttataatattca
attgttctcagggactatcacttcctctttccagtcaatatcgctggtatcaagtacttt
atcaactcggagtatttatctcaagatcatcagtaaaattcttcgaaatgccattgtggt
tgatttggtgtcttccaattcttcaatgtgtcaatatgattttctttttcttcgaggctg
tttattggttcactcctacgattattataatttttgttctcattgttttcgaaggtcttt
tgggaggatctgcttatgtgaacacttacaataaaattcacaaaaaggtcaatcctgacg
tccgagagtactctctgtcagctgcttccatgggaaac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGAGGCTGCTGAAGCCCGGGGAGA 643 687 689 Antisense
GTTCCACAACGGGAGCTTGGACCGC 228 441 733 Antisense
AATTGGTCCACTGTTGTATCTGATG 490 179 774 Antisense
GATGGTTCCACTTGCAACTGTATAC 34 409 795 Antisense
TGTTCTCAGGGACTATCACTTCCTC 78 563 871 Antisense
GTGTCTTCCAATTCTTCAATGTGTC 673 485 996 Antisense
TGATTTTCTTTTTCTTCGAGGCTGT 95 563 1025 Antisense
GCTGTTTATTGGTTCACTCCTACGA 49 295 1045 Antisense
GGAGGATCTGCTTATGTGAACACTT 5 517 1111 Antisense
AATCCTGACGTCCGAGAGTACTCTC 60 169 1159 Antisense
TCTGTCAGCTGCTTCCATGGGAAAC 127 609 1182 Antisense
Sequence Source Affymetrix Proprietary Database