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grch38-heart-genes-sifrim-v1
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public |
CDS region genomic coordinates, along with complement coordinates, for a manually curated set of congenital heart disease (CHD) genes from Sifrim et al. (www.nature.com/articles/ng.3627). Used Supplemental Table 20 here: https://media.nature.com/original/nature-assets/ng/journal/v48/n9/extref/ng.3627-S13.xlsx
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2025-03-25 |
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grch38-eiee-genes-ostrander-v1
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public |
CDS region genomic coordinates, along with complement coordinates, for a set of eiee genes. The eiee gene set comes from a paper on EIEE (Early Infantile Epileptic Encephalopathy) a severe, fatal epileptic syndrome that occurs within the first few months of life. The gene set is a compilation of gene sets from a few different companies, gene panels, as well as one from the U of Chicago. Paper at: https://www.nature.com/articles/s41525-018-0061-8
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2025-03-25 |
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grch37-heart-genes-sifrim-v1
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public |
CDS region genomic coordinates, along with complement coordinates, for a manually curated set of congenital heart disease (CHD) genes from Sifrim et al. (www.nature.com/articles/ng.3627). Used Supplemental Table 20 here: https://media.nature.com/original/nature-assets/ng/journal/v48/n9/extref/ng.3627-S13.xlsx
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2025-03-25 |
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grch37-eiee-genes-ostrander-v1
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public |
CDS region genomic coordinates, along with complement coordinates, for a set of eiee genes. The eiee gene set comes from a paper on EIEE (Early Infantile Epileptic Encephalopathy) a severe, fatal epileptic syndrome that occurs within the first few months of life. The gene set is a compilation of gene sets from a few different companies, gene panels, as well as one from the U of Chicago. Paper at: https://www.nature.com/articles/s41525-018-0061-8
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2025-03-25 |
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hg38-canonical-transcript-features-ensembl-v1
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public |
Gene features from Ensembl Release-100 for protein-coding canonical transcripts based on the APPRIS transcript annotations. Features include gene, transcript, CDS, five_prime_utr, three_prime_utr, exon, start_codon, and stop_codon for all canonical transcripts. Canonical transcripts are determined based on APPRIS annotations. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene annotated by APPRIS are missing from the base gtf file no canonical transcript is chosen and the gene is removed. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Remapped from Ensembl GRCh38 to UCSC hg38
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2025-03-25 |
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hg19-canonical-transcript-features-ensembl-v1
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public |
Gene features from Ensembl Release-75 for protein-coding canonical transcripts based on the APPRIS transcript annotations. Features include gene, transcript, CDS, UTR, exon, start_codon, and stop_codon for all canonical transcripts. Canonical transcripts are determined based on APPRIS annotations. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene annotated by APPRIS are missing from the base gtf file no canonical transcript is chosen and the gene is removed. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Remapped from Ensembl GRCh37 to UCSC hg19
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2025-03-25 |
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grch38-canonical-transcript-features-ensembl-v1
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public |
Gene features from Ensembl Release-100 for protein-coding canonical transcripts based on the APPRIS transcript annotations. Features include gene, transcript, CDS, five_prime_utr, three_prime_utr, exon, start_codon, and stop_codon for all canonical transcripts. Canonical transcripts are determined based on APPRIS annotations. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene annotated by APPRIS are missing from the base gtf file no canonical transcript is chosen and the gene is removed. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Remapped from Ensembl GRCh38 to UCSC hg38
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2025-03-25 |
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grch37-canonical-transcript-features-ensembl-v1
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public |
Gene features from Ensembl Release-75 for protein-coding canonical transcripts based on the APPRIS transcript annotations. Features include gene, transcript, CDS, UTR, exon, start_codon, and stop_codon for all canonical transcripts. Canonical transcripts are determined based on APPRIS annotations. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene annotated by APPRIS are missing from the base gtf file no canonical transcript is chosen and the gene is removed. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
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2025-03-25 |
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hg38-gene-features-gencode-v1
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public |
Comprehensive set of gene anntotations including reference chromosomes, scaffoldings, assebly patches, and alternative loci. Data is specific to GENCODE Release 34 (Ensembl 100). Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine. Remapped from Ensembl GRCh38 to UCSC hg38. (Scaffoldings wihtout UCSC matches are kept with Ensebml ids)
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2025-03-25 |
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hg19-gene-features-gencode-v1
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public |
Comprehensive set of gene anntotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine. Remapped from Ensembl GRCh37 to UCSC hg19
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2025-03-25 |
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grch38-gene-features-gencode-v1
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public |
Comprehensive set of gene anntotations including reference chromosomes, scaffoldings, assebly patches, and alternative loci. Data is specific to GENCODE Release 34 (Ensembl 100). Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine.
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2025-03-25 |
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grch37-gene-features-gencode-v1
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public |
Comprehensive set of gene anntotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine.
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2025-03-25 |
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grch38-self-chain-ucsc-v1
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public |
Self chain alignemnts of the human genome with an improved gap scoring system. Alignemtns point out areas of duplication wihtin the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC. Remapped from UCSC hg38 to Ensembl GRCh37
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2025-03-25 |
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hg38-self-chain-ucsc-v1
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public |
Self chain alignemnts of the human genome with an improved gap scoring system. Alignemtns point out areas of duplication wihtin the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC.
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2025-03-25 |
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hg19-self-chain-ucsc-v1
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public |
Self chain alignemnts of the human genome with an improved gap scoring system. Alignemtns point out areas of duplication wihtin the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC.
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2025-03-25 |
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grch37-self-chain-ucsc-v1
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public |
Self chain alignemnts of the human genome with an improved gap scoring system. Alignemtns point out areas of duplication wihtin the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC. Remapped from UCSC hg19 to Ensembl GRCh37
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2025-03-25 |
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hg38-chrom-mapping-refseq2ucsc-ncbi-v1
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public |
A tab delimited file containing scaffolding ids that map GRCh38 RefSeq to hg38 UCSC scaffoldings. This is specific to patch 13 of the GRCh38 Human genome build. (1st Column = RefSeq ids, 2nd Column = UCSC ids)
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2025-03-25 |
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hg19-chrom-mapping-refseq2ucsc-ncbi-v1
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public |
A tab delimited file containing scaffolding ids that maps GRCh37 RefSeq scaffoldings to hg19 UCSC scaffoldings. This is specific to patch 13 of the GRCh37 Human genome build. (1st column = RefSeq ids, 2nd column = UCSC ids)
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2025-03-25 |
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grch38-chrom-mapping-ucsc2refseq-ncbi-v1
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public |
A tab delimited file containing scaffolding ids that map hg38 UCSC to GRCh38 RefSeq scaffoldings. This is specific to patch 13 of the GRCh38 Human genome build. (1st column = UCSC ids, 2nd Column = RefSeq ids)
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2025-03-25 |
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grch38-chrom-mapping-ensembl2refseq-ncbi-v1
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public |
A tab delimited file containing scaffolding ids that map GRCh38 Ensembl(GenBank) to GRCh38 RefSeq scaffoldings. This is specific to patch 13 of the GRCh38 Human genome build. (1st column = Ensembl ids, 2nd Column = RefSeq ids)
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2025-03-25 |
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grch37-chrom-mapping-ucsc2refseq-ncbi-v1
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public |
A tab delimited file containing scaffolding ids that maps hg19 UCSC scaffoldings to GRCh37 RefSeq scaffoldings. This is specific to patch 13 of the GRCh37 Human genome build. (1st column = UCSC ids, 2nd column = RefSeq ids)
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2025-03-25 |
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grch37-chrom-mapping-refseq2ensembl-ncbi-v1
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public |
A tab delimited file containing scaffolding ids that maps GRCh37 RefSeq scaffoldings to GRCh37 Ensembl(GenBank) scaffoldings. This is specific to patch 13 of the GRCh37 Human genome build. (1st column = RefSeq ids, 2nd column = Ensembl ids)
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2025-03-25 |
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grch37-chrom-mapping-ensembl2refseq-ncbi-v1
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public |
A tab delimited file containing scaffolding ids that maps GRCh37 Ensembl(GenBank) scaffoldings to GRCh37 RefSeq scaffoldings. This is specific to patch 13 of the GRCh37 Human genome build. (1st column = Ensembl ids, 2nd column = RefSeq ids)
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2025-03-25 |
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grch38-chrom-mapping-refseq2ensembl-ncbi-v1
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public |
A tab delimited file containing scaffolding ids that map GRCh38 RefSeq scaffoldings to GRCh38 Ensembl(GenBank) scaffoldings. This is specific to patch 13 of the GRCh38 Human genome build. (1st column = RefSeq ids, 2nd column = Ensembl ids)
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2025-03-25 |
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hg38-autosomal-recessive-genes-blekhman-v1
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public |
CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes deemed to follow autosomal recessive inheritance according to extensive manual curation by Molly Przeworski's group.(https://www.ncbi.nlm.nih.gov/pubmed/18571414).
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2025-03-25 |
