RetrogeneDB ID: retro_shar_791

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864851.1:178856..179399(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRP1
• Ensembl ID: ENSSHAG00000010304
• Aliases: None
• Description: ribosomal RNA processing 1 [Source:HGNC Symbol;Acc:18785]

Sequence

>retro_shar_791
AAAAGATATGGTTGGGAAGAAAGTCAGGTCAAACTACTTCAGGATATCTTAGTGAAAGGACTTTTGCACCCTGACAATCA
AGCACCTCATGGAATAAAGTCCCACTTTATTGACCTATATGGGGAGAAATAAGGAAAGTAGAAGCAAAACAGTTGATAGC
AAATCAAAACCTGAAGTTTATTGTTTCATTCTGAAAAACTGCAGCTAGAACAAAGGATGCTATTTTGCTGTATGATATCA
TCGGGAGTATCTTTGAAGAAATTTTGGAACAAGCTCCCTTTTCCACTGAAGAATTAATACCAGAATTAAGTGCAAACCAA
GAGTAAATTATTAGAACAACAGTGAATTGTCAGAAGCAGACAGGCATAAGATTACCTAGGAAGCAAAAGAAGGGAAAGAA
ATGTAAGAAGTCTTCACCAAGGGAAGATAAAGTCAAAGGGGAAAAAAAGAGTGATGGCAAGGGACATTGGGCTTATCCTT
CAGTTTAACTATAAGAAAATTGCTGATAGACTGGAATGGCCAGCAAGTTAAGGAGCCCTTCCT

Alignment

ORF - retro_shar_791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.15 %
• Parental protein coverage: 56. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KRSGWEESQVELLLDILMKEILHPDSQAPCGIKSHFIDIYLE-ELTKVGAEELTADQNLNFVVPFCKIAS
          KR.GWEESQV.LL.DIL.K..LHPD.QAP.GIKSHFID.Y.E.E..KV.A..L.A.QNL.F.V.F.K.A.
Retrocopy KRYGWEESQVKLLQDILVKGLLHPDNQAPHGIKSHFIDLYGE<EIRKVEAKQLIANQNLKFIVSF*KTAA

Parental  RTKDSTLLYNIVGGIFDAILEQAPFAIEDLIRELNANQEDSELLETESDDMTTIRLHGKQKKGKKGKDSF
          RTKD..LLY.I.G.IF..ILEQAPF..E.LI.EL.ANQE............T.IRL..KQKKGKK.K.S.
Retrocopy RTKDAILLYDIIGSIFEEILEQAPFSTEELIPELSANQE*IIRTTVNCQKQTGIRLPRKQKKGKKCKKSS

Parental  SSEDK-PKVKKQSNGKGHIGRVLQFNYEEIADRLFEMASRQSTP
          ..EDK..K.KK.......IG..LQFNY..IADRL...AS....P
Retrocopy PREDK>SKGKKRVMARD-IGLILQFNYKKIADRLEWPAS*GALP

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_791 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000010304	3 retrocopies	retro_shar_145, retro_shar_282, retro_shar_791 ,