RefSeq Gene
 

RefSeq Gene icd-1

RefSeq: NM_062935.9   Status: Reviewed
Description: Caenorhabditis elegans Transcription factor BTF3 homolog (icd-1), mRNA.
CDS: 5' and 3' incomplete
Entrez Gene: 174090
PubMed on Gene: icd-1
PubMed on Product: Transcription factor BTF3 homolog

Summary of icd-1


mRNA/Genomic Alignments

BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |  2376  100.0%         II     -   6584448   6588655             NM_062935     1  2376  2376

View details of parts of alignment within browser window
.

Position: chrII:6584448-6588655
Genomic Size: 4208
Strand: -
Gene Symbol: icd-1
CDS Start: complete
CDS End: complete

Links to sequence:

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Data last updated at UCSC: 2020-08-18

Description

The RefSeq Genes track shows known C. elegans protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly.

Please visit the Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark).

The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. This page is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu.

  • Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely.
  • Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature.
  • Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box.

Methods

RefSeq RNAs were aligned against the C. elegans genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project.

References

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518

Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979