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grch38-ccds-genes-ucsc-v1
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public |
Consensus Coding Seqeunce (CCDS) high confidence gene annotation from UCSC. The annotation here are high quality manually curated protein-coding regions from the Consensus CDS project. Remapped from UCSC hg38 to Ensembl GRCh38
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2025-03-25 |
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grch37-ccds-genes-ucsc-v1
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public |
Consensus Coding Seqeunce (CCDS) high confidence gene annotation from UCSC. The annotation here are high quality manually curated protein-coding regions from the Consensus CDS project. Remapped from UCSC hg19 to Ensembl GRCh37
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2025-03-25 |
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hg38-ncbi-refseq-genes-ucsc-v1
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public |
NCBI Refseq Genes track from UCSC. Curated and predicated genes from Refseq. Data include protein-coding and non-protein-coding genes. Gene info includes chromosome, transcript coordinates, CDS coordinates, exon coordinates, exon count, strand, gene and transcript ids, etc.
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2025-03-25 |
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hg38-ncbi-refseq-gene-features-ucsc-v1
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public |
Gene features for all curated and predicted annotations from the NCBI Refseq track from UCSC. (GTF). Refseq ALL. Human protein-coding and non-protein-coding genes from NCBI RNA reference seqeunce collection.
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2025-03-25 |
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hg19-ncbi-refseq-genes-ucsc-v1
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public |
NCBI Refseq Genes track from UCSC. Curated and predicated genes from Refseq. Data include protein-coding and non-protein-coding genes. Gene info includes chromosome, transcript coordinates, CDS coordinates, exon coordinates, exon count, strand, gene and transcript ids, etc. Scaffoldings that are not contained in the hg19.genome file are removed
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2025-03-25 |
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hg19-ncbi-refseq-gene-features-ucsc-v1
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public |
Gene features for all curated and predicted annotations from the NCBI Refseq track from UCSC. (GTF). Refseq ALL. Human protein-coding and non-protein-coding genes from NCBI RNA reference seqeunce collection. Scaffoldings that are not contained in the hg19.genome file are removed
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2025-03-25 |
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grch38-ncbi-refseq-genes-ucsc-v1
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public |
NCBI Refseq Genes track from UCSC. Curated and predicated genes from Refseq. Data include protein-coding and non-protein-coding genes. Gene info includes chromosome, transcript coordinates, CDS coordinates, exon coordinates, exon count, strand, gene and transcript ids, etc. Remapped from UCSC hg38 to Ensembl GRCh38
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2025-03-25 |
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grch38-ncbi-refseq-gene-features-ucsc-v1
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public |
Gene features for all curated and predicted annotations from the NCBI Refseq track from UCSC. (GTF). Refseq ALL. Human protein-coding and non-protein-coding genes from NCBI RNA reference seqeunce collection. Remapped from UCSC hg38 to Ensembl GRCh38
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2025-03-25 |
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grch37-ncbi-refseq-genes-ucsc-v1
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public |
NCBI Refseq Genes track from UCSC. Curated and predicated genes from Refseq. Data include protein-coding and non-protein-coding genes. Gene info includes chromosome, transcript coordinates, CDS coordinates, exon coordinates, exon count, strand, gene and transcript ids, etc. Scaffoldings that are not contained in the hg19.genome file are removed. Remapped from UCSC hg19 to Ensembl GRCh37
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2025-03-25 |
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grch37-ncbi-refseq-gene-features-ucsc-v1
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public |
Gene features for all curated and predicted annotations from the NCBI Refseq track from UCSC. (GTF). Refseq ALL. Human protein-coding and non-protein-coding genes from NCBI RNA reference seqeunce collection. Scaffoldings that are not contained in the hg19.genome file are removed. Remapped from UCSC hg19 to Ensembl GRCh37
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2025-03-25 |
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hg38-knowngene-gene-features-ucsc-v1
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public |
Gene features from the 'KnownGene' track from UCSC. (GTF). Features include 5UTR, 3UTR, CDS, exon, start_codon, stop_codon, transcript. Features are comprised of all gene models from GENCODE v32. IDs correspond to the UCSC knowGene IDs.
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2025-03-25 |
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hg19-knowngene-gene-features-ucsc-v1
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public |
Gene features from the 'KnownGene' track from UCSC. (GTF). Features include 5UTR, 3UTR, CDS, exon, start_codon, stop_codon, transcript. Features are comprised of gene predictions based on data from Refseq, GenBank, CCDS, RFam, and tRNA genes tracks. IDs correspond to the UCSC knowGene IDs
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2025-03-25 |
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grch38-knowngene-gene-features-ucsc-v1
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public |
Gene features from the 'KnownGene' track from UCSC. (GTF). Features include 5UTR, 3UTR, CDS, exon, start_codon, stop_codon, transcript. Features are comprised of all gene models from GENCODE v32. IDs correspond to the UCSC knowGene IDs. Remapped from UCSC hg38 to Ensembl GRCh38
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2025-03-25 |
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grch37-knowngene-gene-features-ucsc-v1
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public |
Gene features from the 'KnownGene' track from UCSC. (GTF). Features include 5UTR, 3UTR, CDS, exon, start_codon, stop_codon, transcript. Features are comprised of gene predictions based on data from Refseq, GenBank, CCDS, RFam, and tRNA genes tracks. IDs correspond to the UCSC knowGene IDs. Remapped from UCSC hg19 to Ensembl GRCh37
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2025-03-25 |
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hg38-known-genes-ucsc-v1
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public |
The 'KnownGene' track from UCSC. Comprised of all gene models from GENCODE v32. Includes protein-coding genes, non-coding RNA genes, and pseudo-genes. Gene symbols and gene descriptions have been added to the dataset.
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2025-03-25 |
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hg19-known-genes-ucsc-v1
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public |
The 'KnownGene' track from UCSC. Comprsied of gene predictions based on data from Refseq, GenBank, CCDS, RFam, and tRNA genes tracks. Includes protein-coding genes and non-coding RNA genes. Gene symbols and gene descriptions have been added to the dataset.
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2025-03-25 |
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grch38-known-genes-ucsc-v1
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public |
The 'KnownGene' track from UCSC. Comprised of all gene models from GENCODE v32. Includes protein-coding genes, non-coding RNA genes, and pseudo-genes. Gene symbols and gene descriptions have been added to the dataset. Remapped from UCSC hg38 to Ensembl GRCh38
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2025-03-25 |
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grch37-known-genes-ucsc-v1
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public |
The 'KnownGene' track from UCSC. Comprsied of gene predictions based on data from Refseq, GenBank, CCDS, RFam, and tRNA genes tracks. Includes protein-coding genes and non-coding RNA genes. Gene symbols and gene descriptions have been added to the dataset. Remapped from UCSC hg19 to Ensembl GRCh37
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2025-03-25 |
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hg38-evofold-ucsc-v1
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public |
*Liftover* The evolutionary conserved mRNA secondary structure predictions hosted on UCSC. In bed format. Lifted over from UCSC hg19 to UCSC hg38.
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2025-03-25 |
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grch38-evofold-ucsc-v1
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public |
*Liftover* The evolutionary conserved mRNA secondary structure predictions hosted on UCSC. In bed format. Lifted over from UCSC hg19 to UCSC hg38. Remapped from UCSC hg38 to Ensembl GRCh38
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2025-03-25 |
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hg38-constrained-coding-regions-quinlan-lab-v1
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public |
*LiftOver* Constrained Coding Regions (CCRs): https://www.nature.com/articles/s41588-018-0294-6. Regions of human specific coding constraint presumably under strong purifying selection. Constraint is based on the lack of variation within the gnomAD dataset calibrated by the size and CpG content of the region. Regional Constraint is broken up into Autosomes and the X-Chromosome. Chromosome coordinates and CCR regions are lifted over from GRCh37 to GRCh38 using the Crossmap algorithm. Additionaly, the chromsomes have been remapped from Ensembl GRCh38 to UCSC hg38. Any unmapped regions are removed. Any region split into multiple regions are combined. (NOTE: The genomic coordinates have been remapped, but there has been no QC on the CCR percentiles preservation. It is yet to be determined if the CCR percentiles have been completely preserved during the liftover, but it can be assumed they should be similar based on the little to no change in region sizes.)
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2025-03-25 |
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grch38-constrained-coding-regions-quinlan-lab-v1
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public |
*LiftOver* Constrained Coding Regions (CCRs): https://www.nature.com/articles/s41588-018-0294-6. Regions of human specific coding constraint presumably under strong purifying selection. Constraint is based on the lack of variation within the gnomAD dataset calibrated by the size and CpG content of the region. Regional Constraint is broken up into Autosomes and the X-Chromosome. Chromosome coordinates and CCR regions are lifted over from GRCh37 to GRCh38 using the Crossmap algorithm. Any unmapped regions are removed. Any region split into multiple regions are combined. (NOTE: The genomic coordinates have been remapped, but there has been no QC on the CCR percentiles preservation. It is yet to be determined if the CCR percentiles have been completely preserved during the liftover, but it can be assumed they should be similar based on the little to no change in region sizes.)
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2025-03-25 |
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hg38-phastcons-ucsc-v1
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public |
Conservation scores based on the phastcons HMM algorithm against multi-aligned sequences of 100 different species
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2025-03-25 |
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grch38-phastcons-ucsc-v1
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public |
Conservation scores based on the phastcons HMM algorithm against multi-aligned sequences of 100 different species. Remapped from UCSC hg38 to Ensembl GRCh38
|
2025-03-25 |
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grch37-phastcons-ucsc-v1
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public |
Conservation scores based on the phastcons HMM algorithm against multi-aligned sequences of 100 different species. Remapped from UCSC hg19 to Ensembl GRCh37
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2025-03-25 |
