RetrogeneDB ID: retro_shar_145

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834465.1:1047524..1048023(-)
• Located in intron of: ENSSHAG00000012191

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_145
GGTTTCAGATATTAAAAAATGCTAAAAATATGGAAAGGGCTTTTCTATTGTATGTGGAGGACAAGCCTCCTCTACAAGAG
AAACTTGGAAATATATTTTCCCAGCTTGGACGTGTTTTTTAGAACACAGAAATCCAGCACCTATTTGTTCACACTTTTTG
ACCAATCATGACACATGAGTGCATTAAAGTAGAAACATTGTGCCTGGATAAGTTCTACATGCTGCCTTTGCTTCTGAACC
AGTCCTTTAAGTTATCAAAGAGAACTGGATGGGAAGAAAGTCAGATTGAAGTATTTGTGGATATTCTAATGAAAGAAAAT
TTGCACCCAGACAGTCAGGGACTTTGTGAAGGAAAGTTCTATTTCATTGACATCTACTTAGAAGAATGACTAAAGTTAGA
GCCAAAGAATTTACAGTAGATCAAAACTTGAAATTCATTATTCCATTCTGCAAAATTGCAACTAGGACACAGCATTCTGC
TTTGTTGTATAATATAGTC

Alignment

ORF - retro_shar_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.91 %
• Parental protein coverage: 52.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFSHDELLKIWKGLFYCMWM-QDKPLLQEELGNTISQLIHVFQNTETQHLFVQTFWQTMNREWIGIDRLR
          GF.....LKIWKGLFYCMW.....PL.QE.LGN..SQL..VF.NTE.QHLFV.TF...M..E.I....L.
Retrocopy GFRY*KMLKIWKGLFYCMWR<DKPPL-QEKLGNIFSQLGRVF*NTEIQHLFVHTF*PIMTHECIKVETLC

Parental  LDKFYMLMRLLLNQSFEALKRSGWEESQVELLLDILMKEILHPDSQAPCGIKSHFIDIYLEE-LTKVGAE
          LDKFYML..LLLNQSF...KR.GWEESQ.E...DILMKE.LHPDSQ..C..K..FIDIYLEE..TKV.A.
Retrocopy LDKFYML-PLLLNQSFKLSKRTGWEESQIEVFVDILMKENLHPDSQGLCEGKFYFIDIYLEE<MTKVRAK

Parental  ELTADQNLNFVVPFCKIASRTKDSTLLYNIV
          E.T.DQNL.F..PFCKIA.RT..S.LLYNIV
Retrocopy EFTVDQNLKFIIPFCKIATRTQHSALLYNIV

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_145 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,