RetrogeneDB ID: retro_shar_282

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841201.1:1944773..1945295(+)
• Located in intron of: ENSSHAG00000015819

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_282
AATACAATTTTCCAGTTCATTCAAGTTTTTCAGGATACAGAAACCCAGCAGCTATTTGTTCAGATTTCTTGGTAAACCAT
GAACTGTGAGTGGATTGGAATAGACAGATTGCACTCAGATAAGTTCTACATGCTAACGTACCTGCTTCTGAACCAGTCTT
TCAACTGACTAAAAAGAAATGGGAGAGAGGAAAGTCAGGTTAAACTTATTCTGGATATCCTAATGAAATAAGTTTTGTAC
CCAGACAATCCTGCACCTTATGGAGTAAAGTTTCACTTTATTGATATACACCTGGAAGAACTGACTAAAGAAGGAGCAGA
AGAGCCTACAGTGAAGTTTGTTATTCCATCCTGCAAAACTGCACCCAGAACAAAGAATTCTACTTTTTAGAGAGGTATTT
TTGAAGCAATTTTGGAACAAGCTCCTTTTGCCATTGAAAATTTAATAAGAAGATTAAATACCAAACAAGAGGACAGTGAA
GTGTTAGAAATTAAATTAGATGATACTCCATCTTTAAAATTA

Alignment

ORF - retro_shar_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 56.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NTISQLIHVFQNTETQHLFVQTFWQTMNREWIGIDRLRLDKFYMLMRLLLNQSFEALKRSGWEESQVELL
          NTI.Q.I.VFQ.TETQ.LFVQ..W.TMN.EWIGIDRL..DKFYML..LLLNQSF..LKR.G.EESQV.L.
Retrocopy NTIFQFIQVFQDTETQQLFVQISW*TMNCEWIGIDRLHSDKFYMLTYLLLNQSFN*LKRNGREESQVKLI

Parental  LDILMKEILHPDSQAPCGIKSHFIDIYLEELTKVGAEELTADQNLNFVVPFCKIASRTKDSTLLYNIVGG
          LDILMK..L.PD..AP.G.K.HFIDI.LEELTK.GAEE.T......FV.P.CK.A.RTK.ST....I...
Retrocopy LDILMK*VLYPDNPAPYGVKFHFIDIHLEELTKEGAEEPT----VKFVIPSCKTAPRTKNSTF*RGIFEA

Parental  IFDAILEQAPFAIEDLIRELNANQEDSELLETESDDMTTIRL
          I....LEQAPFAIE.LIR.LN..QEDSE.LE...DD.....L
Retrocopy I----LEQAPFAIENLIRRLNTKQEDSEVLEIKLDDTPSLKL

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_282 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,