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RefSeq Gene
 

RefSeq Gene PPT2-EGFL8

RefSeq: NR_037861.1   Status: Validated
CDS: 3' complete
Entrez Gene: 100532746
PubMed on Gene: PPT2-EGFL8
GeneCards: PPT2-EGFL8
AceView: PPT2-EGFL8
Stanford SOURCE: NR_037861

Summary of PPT2-EGFL8

This locus represents naturally occurring read-through transcription between the neighboring PPT2 (palmitoyl-protein thioesterase 2) and EGFL8 (EGF-like-domain, multiple 8) genes located in the major histocompatibility complex class III region of chromosome 6. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]. ##Evidence-Data-START## Transcript exon combination :: AF020544.1 [ECO:0000332] RNAseq introns :: single sample supports all introns ERS025085, ERS025086 [ECO:0000348] ##Evidence-Data-END##


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 |  2728  100.0%  6_ssto_hap7     +   3469501   3483790             NR_037861     1  2728  2728
browser |  2728  100.0%          6     +  32121776  32136062             NR_037861     1  2728  2728
browser |  2728  100.0%  6_apd_hap1     +   3436514   3450803             NR_037861     1  2728  2728
browser |  2728   99.9%  6_cox_hap2     +   3592444   3606743             NR_037861     1  2728  2728
browser |  1124   99.9%  6_dbb_hap3     +   3400949   3404884             NR_037861     1  1124  2728
browser |  2725   99.9%  6_mann_hap4     +   3464620   3478886             NR_037861     1  2728  2728
browser |  2728  100.0%  6_mcf_hap5     +   3501599   3515891             NR_037861     1  2728  2728
browser |  2728  100.0%  6_qbl_hap6     +   3382789   3397082             NR_037861     1  2728  2728

Position: chr6:32121776-32136062
Band: 6p21.32
Genomic Size: 14287
Strand: +
Gene Symbol: PPT2-EGFL8

Position: chr6_cox_hap2:3592444-3606743
Genomic Size: 14300
Strand: +
Gene Symbol: PPT2-EGFL8

Position: chr6_dbb_hap3:3400949-3404884
Genomic Size: 3936
Strand: +
Gene Symbol: PPT2-EGFL8

Position: chr6_mann_hap4:3464620-3478886
Genomic Size: 14267
Strand: +
Gene Symbol: PPT2-EGFL8

Position: chr6_mcf_hap5:3501599-3515891
Genomic Size: 14293
Strand: +
Gene Symbol: PPT2-EGFL8

Position: chr6_qbl_hap6:3382789-3397082
Genomic Size: 14294
Strand: +
Gene Symbol: PPT2-EGFL8

Position: chr6_ssto_hap7:3469501-3483790
Genomic Size: 14290
Strand: +
Gene Symbol: PPT2-EGFL8

Position: chr6_apd_hap1:3436514-3450803
Genomic Size: 14290
Strand: +
Gene Symbol: PPT2-EGFL8

Links to sequence:

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Data last updated: 2013-05-15

Description

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

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. 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

RefSeq 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 0.1% 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.

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.