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Cluster Members
Consensus/Exemplar

GeneChip Array Information

Probe Set ID

190429_at

GeneChip Array

C. elegans Genome Array

Organism Common Name

Nematode

Probe Design Information

Transcript ID(Array Design)

affy.Ce.8649

Sequence Type

Exemplar sequence

Representative Public ID

R09H10.3 NCBI

Target Description

R09H10.3 /REP_DB=WormBase Gene ID /WP=CE12662 /TR=SW:Q21882 /GB=CAB00872.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=transthyretin 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_069561(11)

Transcript Assignments

Representative Transcript	Description	Matching Probes	Related Probesets by Grade
NM_069561 NCBI	Caenorhabditis elegans R09H10.3 (R09H10.3) mRNA, complete cds.	11/11	None
SNAP00000043240 ENSEMBL	cdna:SNAP chromosome:CEL140:IV:10607851:10608344:1	11/11	None
GENEFINDER00000043250 ENSEMBL	cdna:GeneFinder chromosome:CEL140:IV:10605248:10608344:1	11/11	None
R09H10.3 ENSEMBL	cdna:known chromosome:CEL140:IV:10606932:10608399:1 gene:R09H10.3	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:10607856-10608350(+)	100.0	100.0

Public Domain and Genome References

Gene Title

transthyretin like

Ensembl

R09H10.3

Entrez Gene

187757 Entrez gene

SwissProt

Q21882 EMBL-EBI

WormBase

CE34083 Wormbase

Functional Annotations

Ortholog

ID	Title	Organism
CHICKEN:GGA.10756.1.S1_AT	similar to CG30016-PA	gga
CHICKEN:GGA.13894.1.S1_S_AT	similar to CG30016-PA	gga
MG-U74BV2:110847_AT	RIKEN cDNA 1190003J15 gene	mm
MOE430B:1431786_S_AT	RIKEN cDNA 1190003J15 gene	mm
MOUSE430_2:1431786_S_AT	RIKEN cDNA 1190003J15 gene	mm
MOE430B:1455186_A_AT	RIKEN cDNA 1190003J15 gene	mm
MOUSE430_2:1455186_A_AT	RIKEN cDNA 1190003J15 gene	mm
MU19KSUBC:TC40225_S_AT	RIKEN cDNA 1190003J15 gene, mRNA (cDNA clone MGC:63168 IMAGE:5255010)	mm
RG-U34C:RC_AI236302_AT	similar to transthyretin (4L369) (predicted)	rn
RAE230B:1377660_AT	similar to transthyretin (4L369) (predicted)	rn
RAT230_2:1377660_AT	similar to transthyretin (4L369) (predicted)	rn

Gene Ontology

GO Biological Process (view graph)
ID	Description	Evidence	Links
6810	transport	inferred from electronic annotation	QuickGO AmiGO
GO Molecular Function (view graph)
ID	Description	Evidence	Links
5386	carrier activity	inferred from electronic annotation	QuickGO AmiGO
5496	steroid binding	inferred from electronic annotation	QuickGO AmiGO

Protein Similarities

Method	ID	Description	E-Value
blast	CAB00871	Hypothetical protein R09H10.2 [Caenorhabditis elegans] ref\|NP_501961.1\| R09H10.2 [Caenorhabditis elegans]	1.0E-158
blast	CAE60751	Hypothetical protein CBG04437 [Caenorhabditis briggsae]	1.0E-125
blast	AAB66023	Hypothetical protein C17A2.7 [Caenorhabditis elegans] ref\|NP_494668.1\| C17A2.7 [Caenorhabditis elegans]	1.0E-99
blast	CAB00872	Hypothetical protein R09H10.3 [Caenorhabditis elegans] ref\|NP_501962.2\| R09H10.3 [Caenorhabditis elegans] sp\|Q21882\|TTH1_CAEEL Hypothetical transthyretin-like protein R09H10.3 in chromosome IV	6.0E-75
blast	CAB00872	Hypothetical protein R09H10.3 [Caenorhabditis elegans] ref\|NP_501962.2\| R09H10.3 [Caenorhabditis elegans] sp\|Q21882\|TTH1_CAEEL Hypothetical transthyretin-like protein R09H10.3 in chromosome IV	5.0E-67
blast	AAC48252	Hypothetical protein ZK697.8 [Caenorhabditis elegans] ref\|NP_503496.1\| ZK697.8 [Caenorhabditis elegans] sp\|O44578\|TTH2_CAEEL Hypothetical transthyretin-like protein ZK697.8 in chromosome V	2.0E-59
blast	AAC48252	Hypothetical protein ZK697.8 [Caenorhabditis elegans] ref\|NP_503496.1\| ZK697.8 [Caenorhabditis elegans] sp\|O44578\|TTH2_CAEEL Hypothetical transthyretin-like protein ZK697.8 in chromosome V	3.0E-58
blast	CAE60750	Hypothetical protein CBG04436 [Caenorhabditis briggsae]	1.0E-54

Protein Domains

Database	ID	Description	E-Value
Pfam	IPR000895 EMBL-EBI	Transthyretin	1.4E-60
Pfam	IPR000895 EMBL-EBI	Transthyretin	1.4E-60
Pfam	IPR002485 EMBL-EBI	Protein of unknown function DUF13	1.5E-50
Pfam	IPR000895 EMBL-EBI	Transthyretin	1.4E-60

Trans Membrane
ID	Number Of Domains	Domain Boundaries
GENEFINDER00000043250	1	7-24

Sequence

Target Sequence

>C. ELEGANS:190429_AT
atgacaatcacggaatcggctgttccaactgcttcgatttcggctcacgtcctcgacatt
tctggtggctcaccagctggaggtgttcaaattctcgcctacatccagcaaaacgatgat
tggactaaaatcggatctgaattcacgcaagacaatgggcgtgttgattgggtatctccc
gatttcaccctaatccctggaacctaccgattggtctacatcacggaaccatactacaaa
gcgaagaatgtggagagcttttatccatatgttgaggttgttttcaacattcgtgatgca
acacaacactaccatgttccattgactttgagtcc

BLASTn GenBank NR

Probe Info

Probe Sequence(5'-3')	Probe X	Probe Y	Probe Interrogation Position	Strandedness
ATGACAATCACGGAATCGGCTGTTC	358	45	13	Antisense
TCACGGAATCGGCTGTTCCAACTGC	276	625	20	Antisense
TGGAGGTGTTCAAATTCTCGCCTAC	470	549	90	Antisense
TTCTCGCCTACATCCAGCAAAACGA	367	689	104	Antisense
AATCGGATCTGAATTCACGCAAGAC	589	169	141	Antisense
ATGGGCGTGTTGATTGGGTATCTCC	494	49	167	Antisense
TGATTGGGTATCTCCCGATTTCACC	4	561	177	Antisense
GAGAGCTTTTATCCATATGTTGAGG	252	395	265	Antisense
GTTGTTTTCAACATTCGTGATGCAA	67	437	289	Antisense
GCAACACAACACTACCATGTTCCAT	536	319	310	Antisense
ACCATGTTCCATTGACTTTGAGTCC	587	85	323	Antisense

Sequence Source

Affymetrix Proprietary Database

Description	R09H10.3 /REP_DB=WormBase Gene ID /WP=CE12662 /TR=SW:Q21882 /GB=CAB00872.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=transthyretin like
Cluster	6grp_highest_10_10 > 25 6grp_high1_10_10 > 41 4grp_highest_8_8 > 25 4grp_high_8_8 > 60 6grp_highest_nonorm > 56 6grp_total > 52 4grp_total > 60 6grp_highest_sub > 03 6grp_high1_sub > 03 6grp_total_sub > Hat 6grp_rule_based > S3 4grp_rule_based > L3