Non-Human RefSeq Gene
 

Non-Human RefSeq Gene LOC104711158

RefSeq: NM_001302995.1   Status: Provisional
Description: Camelina sativa tubulin beta-2 chain (LOC104711158), mRNA.
Organism: Camelina sativa
Entrez Gene: 104711158
PubMed on Gene: LOC104711158
PubMed on Product: tubulin beta-2 chain
GeneCards: LOC104711158
AceView: LOC104711158


mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |  1284   74.3%          6     ++  30720507  30724361          NM_001302995     1  1299  1353
browser |  1284   74.3%  6_GL000250v2_alt     ++   2050010   2053864          NM_001302995     1  1299  1353
browser |  1284   74.3%  6_GL000251v2_alt     ++   2200246   2204100          NM_001302995     1  1299  1353
browser |  1284   74.3%  6_GL000252v2_alt     ++   1976357   1980211          NM_001302995     1  1299  1353
browser |  1284   74.3%  6_GL000253v2_alt     ++   2030758   2034612          NM_001302995     1  1299  1353
browser |  1284   74.3%  6_GL000254v2_alt     ++   2064582   2068436          NM_001302995     1  1299  1353
browser |  1284   74.3%  6_GL000255v2_alt     ++   1975619   1979473          NM_001302995     1  1299  1353
browser |  1284   74.3%  6_GL000256v2_alt     ++   2021293   2025147          NM_001302995     1  1299  1353

Position: chr6:30720507-30724361
Band: 6p21.33
Genomic Size: 3855
Strand: +
Gene Symbol: LOC104711158
CDS Start: complete
CDS End: not complete

Position: chr6_GL000250v2_alt:2050010-2053864
Band: 6_GL000250v2_alt
Genomic Size: 3855
Strand: +
Gene Symbol: LOC104711158
CDS Start: complete
CDS End: not complete

Position: chr6_GL000251v2_alt:2200246-2204100
Band: 6_GL000251v2_alt
Genomic Size: 3855
Strand: +
Gene Symbol: LOC104711158
CDS Start: complete
CDS End: not complete

Position: chr6_GL000252v2_alt:1976357-1980211
Band: 6_GL000252v2_alt
Genomic Size: 3855
Strand: +
Gene Symbol: LOC104711158
CDS Start: complete
CDS End: not complete

Position: chr6_GL000253v2_alt:2030758-2034612
Band: 6_GL000253v2_alt
Genomic Size: 3855
Strand: +
Gene Symbol: LOC104711158
CDS Start: complete
CDS End: not complete

Position: chr6_GL000254v2_alt:2064582-2068436
Band: 6_GL000254v2_alt
Genomic Size: 3855
Strand: +
Gene Symbol: LOC104711158
CDS Start: complete
CDS End: not complete

Position: chr6_GL000255v2_alt:1975619-1979473
Band: 6_GL000255v2_alt
Genomic Size: 3855
Strand: +
Gene Symbol: LOC104711158
CDS Start: complete
CDS End: not complete

Position: chr6_GL000256v2_alt:2021293-2025147
Band: 6_GL000256v2_alt
Genomic Size: 3855
Strand: +
Gene Symbol: LOC104711158
CDS Start: complete
CDS End: not complete

Links to sequence:

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Data last updated: 2019-10-03


p12 Note: Includes annotations on GRCh38.p12 patch sequences

Description

This track shows known protein-coding and non-protein-coding genes for organisms other than human, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly.

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.

  • 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. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.
  • 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

The RNAs were aligned against the human 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 0.5% of the best and at least 25% 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, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018

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