RetrogeneDB ID: retro_shar_516

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849750.1:141005..141473(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM109
• Ensembl ID: ENSSHAG00000009642
• Aliases: None
• Description: transmembrane protein 109 [Source:HGNC Symbol;Acc:28771]

Sequence

>retro_shar_516
AGATCGGGCGGCAGCTTCGTGATGGGGCGAATTCCGCCCCAGGCCCTCCTGGTGGCCTCCGTGGCCCTCCTCCTCGCCCT
GCACGCGGCAAGCTCCCACAGGGACTTCCACTTTAGAAAACCCCAGAAGAAGGACCCCGTGGCCGACTTCCTGTCCCAAA
CAGCGGCGGCCATTCGGGAGGCGATGGAAGCGCTGCTCGGGCCCGAGCTCGTGCACTTCCTGGCCGAGATCTTGCCGACC
GTCTCTTCGGTCCTCTCGGAGTTTTGCTTCACGCTCTCCCGGGTCTCCGCGCAGCTGCTGGACGCCGTGGGGCTGGAGGG
GGACCACCTCACGCGGGCCTTGAAGCTCAGCCCTGACGAAGTTCAGGTCCTCCTCCTGTGGGGCTTCGGGGCCCTCGCGG
CCTACTGGATGCTGGCCCTGCTGGGCCAGGGCTTGAAGCTGCTCCTCTTCCTCGTGGCCTTTGTGGTG

Alignment

ORF - retro_shar_516 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.12 %
• Parental protein coverage: 65.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLGSRFLMGRAVPKALLAAFVALLLVLHVANSQQDFQSRKQQKDHPPTDFLSQTGWAIRETMDAWIGPEV
          R.G..F.MGR..P.ALL.A.VALLL.LH.A.S..DF..RK.QK..P..DFLSQT..AIRE.M.A..GPE.
Retrocopy RSGGSFVMGRIPPQALLVASVALLLALHAASSHRDFHFRKPQKKDPVADFLSQTAAAIREAMEALLGPEL

Parental  MHVVAETLSQVLWAVSSALSVACFALSGISAQLLSAMGLHGEHLTQGLKLSPGQVQTFLLWGAGALVAYW
          .H..AE.L..V....SS.LS..CF.LS..SAQLL.A.GL.G.HLT..LKLSP..VQ..LLWG.GAL.AYW
Retrocopy VHFLAEILPTV----SSVLSEFCFTLSRVSAQLLDAVGLEGDHLTRALKLSPDEVQVLLLWGFGALAAYW

Parental  VLALL---LGLLLALLGRIL
          .LALL...L.LLL.L.....
Retrocopy MLALLGQGLKLLLFLVAFVV

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_516 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000009642	1 retrocopy	retro_shar_516 ,