RetrogeneDB ID: retro_shar_812

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL865182.1:199794..200002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000000550
• Aliases: None
• Description: None

Sequence

>retro_shar_812
GGAACCTCAGGTTTTGGAAACAGTGGGACAAGCAAGCCAATGAAGGATATTGAAGTTACAGCTTCTTCTGATAACGGTAT
TGGATGTCTTTATTTTAGCCTGCCTATATTGCCAAGGAACTTTTATTACAGAAAGCTGGGTCAATGATATTCGATGTTGG
GAAGTTCATGATAATGGCCAAACTATTCCAAAAATTCAGCAGACGCAC

Alignment

ORF - retro_shar_812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.75 %
• Parental protein coverage: 52.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTSMFGSTTTDNHNPMKDIEVTSSPDDSIGCLSFSPPTLP-GNFLIAGSWANDVRCWEVQDNGQTIPKAQ
          GTS.FG...T....PMKDIEVT.S.D..IGCL.FS.P.LP.G.F.I..SW.ND.RCWEV.DNGQTIPK.Q
Retrocopy GTSGFGNSGTSK--PMKDIEVTASSDNGIGCLYFSLPILP>GTF-ITESWVNDIRCWEVHDNGQTIPKIQ

Parental  QMH
          Q.H
Retrocopy QTH

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_812 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000001585	2 retrocopies	retro_ocun_1819, retro_ocun_646,
Otolemur garnettii	ENSOGAG00000014649	2 retrocopies	retro_ogar_1400, retro_ogar_2829,
Ochotona princeps	ENSOPRG00000000228	1 retrocopy	retro_opri_1149,
Sarcophilus harrisii	ENSSHAG00000000550	1 retrocopy	retro_shar_812 ,
Sarcophilus harrisii	ENSSHAG00000002438	1 retrocopy	retro_shar_811,
Sarcophilus harrisii	ENSSHAG00000010372	1 retrocopy	retro_shar_358,