RetrogeneDB ID: retro_shar_71

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834418.1:540685..541021(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000009404
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: COX6A2
• Ensembl ID: ENSSHAG00000014247
• Aliases: None
• Description: cytochrome c oxidase subunit VIa polypeptide 2 [Source:HGNC Symbol;Acc:2279]

Sequence

>retro_shar_71
ATGATGGCAACCACAGGCCGGAGAGTGCTGACCTTCCTGGGCCAGAGCCGCGCGTTAGCCGGGCGGACGTTCTTAAGCAG
CTCTTCAATGGAGGGCATCGAGGAGGGATCGGCCCGCATGTGGAAGATGCTCACTTTTGGTCTTGCGCTCCCCGGCGTGA
TGGTCAGTATGATAAACTGCTACTTGAAAGCAAAGGATCATCCCAGGAGACACAAGTTCGTCCCGTACAGCCACCTCCGG
ATCCGGACCAAGCCCTTCCCCTGGGGAGATGGTAACCACACTCTCTTTCATAACAGACGAGTCAATCCTCTGCCAACTGG
TTATGAAGATGACTAA

Alignment

ORF - retro_shar_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.29 %
• Parental protein coverage: 86.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LATAAKEEHGGAGAKTWRVLTLVLALPAVAVCTLNSWLHSGHH-ERPEFIPYAHLRIRTKPYAWGDGNHT
          L.....E......A..W..LT..LALP.V.V...N..L....H..R..F.PY.HLRIRTKP..WGDGNHT
Retrocopy LSSSSMEGIEEGSARMWKMLTFGLALPGVMVSMINCYLKAKDHPRRHKFVPYSHLRIRTKPFPWGDGNHT

Parental  LFHNPHVNPLPTGYE
          LFHN..VNPLPTGYE
Retrocopy LFHNRRVNPLPTGYE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_71 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016284	1 retrocopy	retro_amel_34,
Sarcophilus harrisii	ENSSHAG00000014247	1 retrocopy	retro_shar_71 ,