RetrogeneDB ID: retro_shar_431

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842571.1:178846..179326(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TMEM159
• Ensembl ID: ENSSHAG00000005768
• Aliases: None
• Description: transmembrane protein 159 [Source:HGNC Symbol;Acc:30136]

Sequence

>retro_shar_431
ATGGTGAAAATGGAGACCTCCAGTACGTCCAAAGATTTGCAGGAGCTTCAGAGGAAGCTAGTTTAATTGATCAATTCCAT
CCAGAGCAACTCTAAGGTGATTGCCTTTATGAACTCTCCAGTTGGTCAATACCTAGATAAACGTCCCTTTGTTGCCTTAA
CCTTGCTGATGTTCATTATGGTATCTTCCATTCCTGTTGGATTCTTCCTGTTGCTTGTGGTCTTGATGTCTCTGGCACCC
TGTGTTGGAGTTATATTAGTGGAAGGATTCGTTATATCTGTGGGCAGCCTCACCTTGCTCTGTGTACTGTGTGGCTTGGG
TTTCGTGTCCCTGGCCATATCTGGAACACTCAGTGTGTGCTACGTGGTGCTCTCGAACCTCACCAACTATTGGTTCTCTT
TCAGCACGCTAAAGCATCAGCAAATCCTTGGAAACAAGTGCCCAGTGACCGTCCAAAATCCCGACTCTACAAGACATAAC

Alignment

ORF - retro_shar_431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVKMETSSTSKDLQELQRKLVSLINSIQSNSKVIAFMNSPVGQYLDKHPFVALTLLMFIMVSSIPVGFFL
          MVKMETSSTSKDLQELQRKLV.LINSIQSNSKVIAFMNSPVGQYLDK.PFVALTLLMFIMVSSIPVGFFL
Retrocopy MVKMETSSTSKDLQELQRKLV*LINSIQSNSKVIAFMNSPVGQYLDKRPFVALTLLMFIMVSSIPVGFFL

Parental  LLVVLMSLAACVGVILVEGFVISVGGLTLLCVLCGLGFVSLAISGTLSVCYVVLSSLTNYWFSFSTLKHQ
          LLVVLMSLA.CVGVILVEGFVISVG.LTLLCVLCGLGFVSLAISGTLSVCYVVLS.LTNYWFSFSTLKHQ
Retrocopy LLVVLMSLAPCVGVILVEGFVISVGSLTLLCVLCGLGFVSLAISGTLSVCYVVLSNLTNYWFSFSTLKHQ

Parental  QILGNKCPVTVQNPDSTRHD
          QILGNKCPVTVQNPDSTRH.
Retrocopy QILGNKCPVTVQNPDSTRHN

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_431 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
Echinops telfairi	ENSETEG00000007187	1 retrocopy	retro_etel_1773,
Sarcophilus harrisii	ENSSHAG00000005768	1 retrocopy	retro_shar_431 ,