Non-Tree shrew RefSeq Gene

Non-Tree shrew RefSeq Gene pax9.L

RefSeq: NM_001174014.2   Status: Validated
Description: Xenopus laevis paired box 9 L homeolog (pax9.L), mRNA.
Organism: Xenopus laevis
UCSC browser: NM_001174014 on African clawed frog (xenLae2)
CDS: 3' complete
Entrez Gene: 100381067
PubMed on Gene: pax9.L
PubMed on Product: paired box 9 L homeolog

Summary of pax9.L

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
browser |   918   77.9%  149545.1-136892     ++      3931     17492          NM_001174014   152  1135  2610
browser |   296   77.4%  139898.1-281199     +-    195397    202650          NM_001174014   164  1592  2610

Position: scaffold_149545.1-136892:3931-17492
Genomic Size: 13562
Strand: +
Gene Symbol: pax9.L
CDS Start: not complete
CDS End: not complete

Position: scaffold_139898.1-281199:195397-202650
Genomic Size: 7254
Strand: -
Gene Symbol: pax9.L
CDS Start: not complete
CDS End: not complete

Links to sequence:

Data schema/format description and download

Go to Other RefSeq track controls

Data last updated at UCSC: 2020-08-20


This track shows known protein-coding and non-protein-coding genes for organisms other than tree shrew, 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.
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The RNAs were aligned against the tree shrew 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.


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


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