RetrogeneDB ID: retro_shar_146

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834465.1:1186724..1187249(-)
• Located in intron of: ENSSHAG00000012191

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP6C
• Ensembl ID: ENSSHAG00000008282
• Aliases: None
• Description: protein phosphatase 6, catalytic subunit [Source:HGNC Symbol;Acc:9323]

Sequence

>retro_shar_146
AATGAGTATCAGATAAACTATGGGAATGTTATTGCCTGGAGATACTGTACTAAAATTTTATATATGATTACAGTTGCAGC
TTTTGTTGACTAGCAGATTTTTGCTTATGTGGTGCTCTCTTTCTGAACATGAAAACACTGAATCAAATATGAACCAATGA
ACAGAATCAGGAAATTCCTCGCAAAAGAGCATTTTGTGCCTTGGTATGGTCAGGTTCTAAAGAGATTGATACTTGAACAA
TTGGAACAGATTGGCTTTTTTGCAATGAAGGTCACAGAGGAGGCTGTTTATTTCAACAACTTAAAACTCATTTGTAGAGG
ATGTCAACTGGTGCATGAAGGGCATAAGATTTACATTTGAAGAAAAGCCTGTGACAATATGGTTAGCTCTCAATTATTGT
TACCATTGTAGAAATATACCTTAATTCTGGTAGTAGAAACAAATTCAAGAGAATCAAATTTATGCTGGACACTTTCAGAT
TTGGAATATATAATTCCTTCTAGAATGACTACATCATGTTTTCTT

Alignment

ORF - retro_shar_146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.64 %
• Parental protein coverage: 62.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DECQTKYGNANAWRYCTKVFDMLTVAALIDEQI-LCVHGGLSPDIKTLDQIRTIERNQEIPHKGAFCDLV
          .E.Q..YGN..AWRYCTK...M.TVAA..D.QI..C..G.L....KTL.QI.T.E.NQEIP.K.AFC.LV
Retrocopy NEYQINYGNVIAWRYCTKILYMITVAAFVD*QI<FCLCGALFLNMKTLNQI*TNEQNQEIPRKRAFCALV

Parental  WSDPEDVDTWAISPRGAGWL-FGAKVTNEFVHINNLKLICRAHQLVHEGYK-FMFDEKLVTVWSAPNYCY
          WS.....DT..I...G..WL.F..KVT.E.V..NNLKLICR..QLVHEG.K.F.F.EK.VT.W.A.NYCY
Retrocopy WSGSKEIDT*TI---GTDWL>FAMKVTEEAVYFNNLKLICRGCQLVHEGHK>FTFEEKPVTIWLALNYCY

Parental  RCGNI-ASIMVFKDVNTREPKLFRAVPDSERVIPPRTTTPYFL
          .C.NI...I.V....N.RE..L.....D.E..IP.R.TT..FL
Retrocopy HCRNI<TLILVVE-TNSRESNLCWTLSDLEYIIPSRMTTSCFL

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_146 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	ENSCHOG00000012357	3 retrocopies	retro_chof_1759, retro_chof_183, retro_chof_608,
Dasypus novemcinctus	ENSDNOG00000015319	1 retrocopy	retro_dnov_1700,
Erinaceus europaeus	ENSEEUG00000010197	1 retrocopy	retro_eeur_706,
Macaca mulatta	ENSMMUG00000020549	1 retrocopy	retro_mmul_698,
Rattus norvegicus	ENSRNOG00000015145	1 retrocopy	retro_rnor_2074,
Sarcophilus harrisii	ENSSHAG00000008282	1 retrocopy	retro_shar_146 ,
Sus scrofa	ENSSSCG00000005600	1 retrocopy	retro_sscr_243,