RetrogeneDB ID: retro_shar_261

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL835710.1:5785..6090(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD10
• Ensembl ID: ENSSHAG00000001698
• Aliases: None
• Description: COMM domain containing 10 [Source:HGNC Symbol;Acc:30201]

Sequence

>retro_shar_261
GTCAAAAGAGGAAAGTTCCTTATTTATATAGTAGATATGGGAAGATTGTTTCAATTGCTTGTATAAATTCTTCAGAAACT
TCCCTTGAAATCCGAGAATAGCTTTAATATTGAGGAAGAAGAAAAATTCCAAACTGTGTTTTTACTAGAGGAACCTGACC
TTCATTTAATCCCTGAAACTATATCATTTATTTGGGGGCAAGTTGTTTATTATAATGTGAAACAAATACCTCTGAAACAA
GAATGTGGGAGCATTCATCTCGGTTAAGACAAAGACAAGCATTTGCCAGTGCTTGGGTCAACATA

Alignment

ORF - retro_shar_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.34 %
• Parental protein coverage: 75.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKKAVSLVNEVDTGRFPRLLTRILQKLHLKTENSFSEEEEEKLQAAFSLEKQDLHLVLETISFILEQAVY
          .K....L...VD.GR...LL..ILQKL.LK.ENSF..EEEEK.Q..F.LE..DLHL..ETISFI..Q.VY
Retrocopy VKRGKFLIYIVDMGRLFQLLV*ILQKLPLKSENSFNIEEEEKFQTVFLLEEPDLHLIPETISFIWGQVVY

Parental  HNVKPAVLQQQLENIHLSQDK-AEAFASAWTSM
          .NVK...L.Q....IHL..DK...AFASAW...
Retrocopy YNVKQIPLKQECGSIHLG*DK<RQAFASAWVNI

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_261 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008311	2 retrocopies	retro_chof_1462, retro_chof_1585,
Cavia porcellus	ENSCPOG00000020474	1 retrocopy	retro_cpor_337,
Loxodonta africana	ENSLAFG00000011885	1 retrocopy	retro_lafr_142,
Microcebus murinus	ENSMICG00000006173	2 retrocopies	retro_mmur_1132, retro_mmur_607,
Myotis lucifugus	ENSMLUG00000010780	1 retrocopy	retro_mluc_2087,
Sarcophilus harrisii	ENSSHAG00000001698	1 retrocopy	retro_shar_261 ,
Tupaia belangeri	ENSTBEG00000004061	1 retrocopy	retro_tbel_3381,