Non-Human RefSeq Gene
 

Non-Human RefSeq Gene TUB5

RefSeq: NM_101856.3   Status: Reviewed
Description: Arabidopsis thaliana tubulin beta-5 chain (TUB5), mRNA.
Organism: Arabidopsis thaliana
Entrez Gene: 838590
PubMed on Gene: TUB5
PubMed on Product: tubulin beta-5 chain
GeneCards: TUB5
AceView: TUB5


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 |  1299   70.9%          6     +-   3224784   3227546             NM_101856   349  1659  2015
browser |  1329   71.4%          6     ++  30720504  30724391             NM_101856   349  1683  2015
browser |  1284   71.2%  6_GL000250v2_alt     ++   2050007   2053894             NM_101856   349  1683  2015
browser |  1269   71.4%  6_GL000251v2_alt     ++   2200243   2204130             NM_101856   349  1683  2015
browser |  1224   71.2%  6_GL000252v2_alt     ++   1976354   1980241             NM_101856   349  1683  2015
browser |  1329   71.4%  6_GL000253v2_alt     ++   2030755   2034642             NM_101856   349  1683  2015
browser |  1329   71.4%  6_GL000254v2_alt     ++   2064579   2068466             NM_101856   349  1683  2015
browser |  1269   71.4%  6_GL000255v2_alt     ++   1975616   1979503             NM_101856   349  1683  2015
browser |  1329   71.4%  6_GL000256v2_alt     ++   2021290   2025177             NM_101856   349  1683  2015

Position: chr6:3224784-3227546
Band: 6p25.2
Genomic Size: 2763
Strand: -
Gene Symbol: TUB5
CDS Start: not complete
CDS End: complete

Position: chr6:30720504-30724391
Band: 6p21.33
Genomic Size: 3888
Strand: +
Gene Symbol: TUB5
CDS Start: complete
CDS End: not complete

Position: chr6_GL000250v2_alt:2050007-2053894
Band: 6_GL000250v2_alt
Genomic Size: 3888
Strand: +
Gene Symbol: TUB5
CDS Start: complete
CDS End: not complete

Position: chr6_GL000251v2_alt:2200243-2204130
Band: 6_GL000251v2_alt
Genomic Size: 3888
Strand: +
Gene Symbol: TUB5
CDS Start: complete
CDS End: not complete

Position: chr6_GL000252v2_alt:1976354-1980241
Band: 6_GL000252v2_alt
Genomic Size: 3888
Strand: +
Gene Symbol: TUB5
CDS Start: complete
CDS End: not complete

Position: chr6_GL000253v2_alt:2030755-2034642
Band: 6_GL000253v2_alt
Genomic Size: 3888
Strand: +
Gene Symbol: TUB5
CDS Start: complete
CDS End: not complete

Position: chr6_GL000254v2_alt:2064579-2068466
Band: 6_GL000254v2_alt
Genomic Size: 3888
Strand: +
Gene Symbol: TUB5
CDS Start: complete
CDS End: not complete

Position: chr6_GL000255v2_alt:1975616-1979503
Band: 6_GL000255v2_alt
Genomic Size: 3888
Strand: +
Gene Symbol: TUB5
CDS Start: complete
CDS End: not complete

Position: chr6_GL000256v2_alt:2021290-2025177
Band: 6_GL000256v2_alt
Genomic Size: 3888
Strand: +
Gene Symbol: TUB5
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