RetrogeneDB ID: retro_shar_663

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856964.1:2492431..2493181(-)
• Located in intron of: ENSSHAG00000016595

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM70A
• Ensembl ID: ENSSHAG00000007111
• Aliases: None
• Description: translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:11985]

Sequence

>retro_shar_663
ATACCATTTTCACAGTTCATTAAATCTTACTTTAGTTTCTTCATTGATAATATTCTCTCAGCCTATGCTTAAAGAAGAGA
AGGCTAATGAAGATAAAGACAAGGAAGGGGAAACCTTAGAAATAAAAGAAAACTGGCTATATAAAGGCCAAACAATACAT
GGAAGGAGAAAACAATGATAAATAAGTGAGGGCACAAAAGAAATAGAAGCACAAGATTAATATACAGCCAAAGTGTTGAT
GCTATAAGTCAACTTCTAATTCTTGTGGGCAATGTCAATGTAGTCAAGACAGATTTAGATCAGGTCATCAGCATGGAAGA
AGCTAATGTAAAGCTTTGAGCAAATGCCCAGATAAAAAGAACCAGTATATATATGCCATAACAGCAACCTTTGATCTACA
CTCAGAATTTAAACACATTTGCTGTTATTGATTCCCAGAATGCAGATGTGTATCATTACCAAATATAATTATAATCTTTT
TTGATCAGGTTGAAGAAACAGTGGCAGATTTTATGAATATATTAAATTATAACCTGATTCTACTCTGGCCCAAACTCAGA
AGTGTTTTGTATTGTATCATTAAGTTTACACAGAAACAGTTCTTTACAAGTCCAGATTGCTTTGAAAGACTTTGAGGAAG
TCATAAAGAAATTTCTAAGATGTGCTGAAGATTATACATTATATACCCAGGCATTGACAGATCAGCAACCAATTGATAAA
GGTGAAGAAATACATAAAAAATGTATGAAC

Alignment

ORF - retro_shar_663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.6 %
• Parental protein coverage: 50.7 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPSPQFIKSYFSSFTDD-IISQPMLKGEKSDEDKDKEGEALEVRENSGYLKAKQYMEEENYDKIISECTK
          .P..QFIKSYF.SF..D.I.SQPMLK.EK..ED..K..E..........L...Q..........ISE.TK
Retrocopy IPFSQFIKSYF-SFFID>IFSQPMLKEEKANED--KDKEGETLEIKENWLYKGQTIHGRRKQ**ISEGTK

Parental  EIDARGKYTAEALLLRATF-YLLIGNANAAKPDLDQVISMEDANVKLRANALIKRGSMYMQQQQPLLSTQ
          EI.A...YTA..L.L...F...L.GN.N..K.DLDQVISME.ANVKL.ANA.IKR.S.YM..QQPL..TQ
Retrocopy EIEAQD*YTAKVLML*VNF<LILVGNVNVVKTDLDQVISMEEANVKL*ANAQIKRTSIYMP*QQPLIYTQ

Parental  DFNMAADIDPQNADVYHHR-GQLKILLDQVEEAVAD-FDECIRLRPDSALAQAQKCFALYRQAYT-GNNS
          ..N..A.ID.QNADVYH.......I..DQVEE.VAD.F.E.I.L.PDS.LAQ.QKCF.LY...YT..N.S
Retrocopy NLNTFAVIDSQNADVYHYQ<NIIIIFFDQVEETVAD<FYEYIKL*PDSTLAQTQKCFVLYH*VYT<RNSS

Parental  TQVQAAMKGFEDVIKKFPRCAEGYALYAQALTDQQQFGKADEMYDKCID
          .QVQ.A.K.FE.VIKKF.RCAE.Y.LY.QALTDQQ...K..E...KC..
Retrocopy LQVQIALKDFEEVIKKFLRCAEDYTLYTQALTDQQPIDKGEEIHKKCMN

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_663 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
Rattus norvegicus	ENSRNOG00000001640	1 retrocopy	retro_rnor_2367,
Sarcophilus harrisii	ENSSHAG00000007111	1 retrocopy	retro_shar_663 ,