Non-Human RefSeq Gene
 

Non-Human RefSeq Gene Tub1

RefSeq: NM_001190398.1   Status: Provisional
Description: Acyrthosiphon pisum tubulin beta-1 (Tub1), mRNA.
Organism: Acyrthosiphon pisum
Entrez Gene: 100168148
PubMed on Gene: Tub1
PubMed on Product: tubulin beta-1
GeneCards: Tub1
AceView: Tub1


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 |  1331   75.0%          6     ++  30720501  30724391          NM_001190398    57  1391  1534
browser |  1331   75.0%  6_GL000250v2_alt     ++   2050004   2053894          NM_001190398    57  1391  1534
browser |  1331   75.0%  6_GL000251v2_alt     ++   2200240   2204130          NM_001190398    57  1391  1534
browser |  1331   75.0%  6_GL000252v2_alt     ++   1976351   1980241          NM_001190398    57  1391  1534
browser |  1331   75.0%  6_GL000253v2_alt     ++   2030752   2034642          NM_001190398    57  1391  1534
browser |  1331   75.0%  6_GL000254v2_alt     ++   2064576   2068466          NM_001190398    57  1391  1534
browser |  1331   75.0%  6_GL000255v2_alt     ++   1975613   1979503          NM_001190398    57  1391  1534
browser |  1331   75.0%  6_GL000256v2_alt     ++   2021287   2025177          NM_001190398    57  1391  1534
browser |  1286   75.8%          9     ++ 137241361 137243508          NM_001190398    63  1352  1534

Position: chr6_GL000256v2_alt:2021287-2025177
Band: 6_GL000256v2_alt
Genomic Size: 3891
Strand: +
Gene Symbol: Tub1
CDS Start: complete
CDS End: not complete

Position: chr6_GL000253v2_alt:2030752-2034642
Band: 6_GL000253v2_alt
Genomic Size: 3891
Strand: +
Gene Symbol: Tub1
CDS Start: complete
CDS End: not complete

Position: chr6_GL000251v2_alt:2200240-2204130
Band: 6_GL000251v2_alt
Genomic Size: 3891
Strand: +
Gene Symbol: Tub1
CDS Start: complete
CDS End: not complete

Position: chr6_GL000252v2_alt:1976351-1980241
Band: 6_GL000252v2_alt
Genomic Size: 3891
Strand: +
Gene Symbol: Tub1
CDS Start: complete
CDS End: not complete

Position: chr6_GL000250v2_alt:2050004-2053894
Band: 6_GL000250v2_alt
Genomic Size: 3891
Strand: +
Gene Symbol: Tub1
CDS Start: complete
CDS End: not complete

Position: chr6:30720501-30724391
Band: 6p21.33
Genomic Size: 3891
Strand: +
Gene Symbol: Tub1
CDS Start: complete
CDS End: not complete

Position: chr6_GL000255v2_alt:1975613-1979503
Band: 6_GL000255v2_alt
Genomic Size: 3891
Strand: +
Gene Symbol: Tub1
CDS Start: complete
CDS End: not complete

Position: chr6_GL000254v2_alt:2064576-2068466
Band: 6_GL000254v2_alt
Genomic Size: 3891
Strand: +
Gene Symbol: Tub1
CDS Start: complete
CDS End: not complete

Position: chr9:137241361-137243508
Band: 9q34.3
Genomic Size: 2148
Strand: +
Gene Symbol: Tub1
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