Variant in the RFWD3 Gene Associated with PATN1, a Modifier of Leopard Complex Spotting

Experiment ID:ERP005568
Technology:RNA-Seq
Description:Leopard Complex spotting (LP), the result of an incompletely dominant mutation in TRPM1, produces a collection of unique pigmentation patterns in the domestic horse. While the LP mutation allows for expression of the various patterns, other loci are responsible for modification of the extent of white. Pedigree analysis of families segregating for high levels of patterning (80-100% white hair coat) indicated a single dominant gene (PATN1) as a major effect modifier for LP. Linkage analysis identified a 16 Mbp region on ECA3p associated with PATN1. Whole transcriptome sequencing of skin samples from horses with and without the PATN1 allele was performed to identify genic SNPs for fine mapping. Two Sequenom assays were utilized to genotype 192 individuals from five LP-containing breeds. The initial panel highlighted a 1.6 Mbp region without a clear candidate gene. In the second round of fine-mapping, a SNP in the 3' UTR of RING finger and WD repeat domain 3 (RFWD3) reached a significance level of p=1.063x10-39. Sequencing of RFWD3 did not identify any coding polymorphisms specific to the PATN1 horses. Genotyping of an additional 52 LP animals increased this association to a p-value of 4.68x10-56. An additional 166 horses of breeds not segregating for LP did not contain the PATN1-associated allele. This variant is a strong candidate for PATN1 and may be used for genotyping lp/lp animals.
Source:ERP005568 SRA
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Bulk RNA-Seq processed expression values in Equus caballus

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Library ID
Identifier of the RNA-Seq library
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
ERX442542UBERON:0000014 zone of skinskinUBERON:0000104 life cycleNANANANANAEquus caballusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100single3413391218906899001842920358Browse results
ERX442543UBERON:0000014 zone of skinskinUBERON:0000104 life cycleNANANANANAEquus caballusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100single3029232016426153001819220222Browse results
ERX442544UBERON:0000014 zone of skinskinUBERON:0000104 life cycleNANANANANAEquus caballusNAIlluminaIllumina HiSeq 2000FULL_LENGTH100single4108331028498481001774019995Browse results
ERX913361UBERON:0000014 zone of skinskinUBERON:0000104 life cycleNAmaleNANANAEquus caballusNAIlluminaIllumina Genome Analyzer IIxFULL_LENGTH81paired83734773005775001480718147.5Browse results

Showing 1 to 4 of 4 entries

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