RetrogeneDB ID: retro_shar_633

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856866.1:156088..156656(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL4
• Ensembl ID: ENSSHAG00000008539
• Aliases: None
• Description: mitochondrial ribosomal protein L4 [Source:HGNC Symbol;Acc:14276]

Sequence

>retro_shar_633
GAGTTCCCAGTTCCCACGCACCAGATGCCAAGTAAACCTGGGTAGAATCCCTTTGTGACTGTGAAGAAATACACTTGGGC
CTGGCTGACCTGAACCCCAATGTATTCTCTGTGGTACCCCAGCTGGATATTCTATATGAGATTGCCACATGGCAGAAGAA
CTTCAAAAGAATTAATTATGTCAAAATCAGGACATGGACAGATATAAGAGGCAGTAGGAGGAAGCCCTAGTAGCAGAAAG
TTTCAGGCCAGGACAGGCTGGGAGTATCCATTCCCAAATCTGGCAAGAAGGTAGTATTGCCTGTGGTCCACAGAGTCCAA
TTAGCTACTACTATATCTTATCTATGAAGGTTTGAATGTTTGCCCTCAAGGTGGCCCTTATAGTCAAGCTGATGCAGGAT
GAGCTTCATATGGTAGATTTCTTGGAGCTGCCAGTGTCAGACACAAGATATTTGTTAGACCTGGCTCGGCACCGTGTTAG
AGACTCTGTTGTCCTTGTTGATATAGATGAGGAGACACCTCAGAATGTTATTTCTGCTGTATCCAACCTAAAGAGCATCA
GTCTGGTA

Alignment

ORF - retro_shar_633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.18 %
• Parental protein coverage: 64.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELPVPVHRGPVQ-AWVESLRGYEETRLGLADLHPDVFSVAPRLDILHEVAIWQKNFKRISYAKTKTRAEV
          E.PVP.H..P....WVESL...EE..LGLADL.P.VFSV.P.LDIL.E.A.WQKNFKRI.Y.K..T....
Retrocopy EFPVPTHQMPSK<TWVESLCDCEEIHLGLADLNPNVFSVVPQLDILYEIATWQKNFKRINYVKIRTWTDI

Parental  RGGGRKPWRQKGSGRAR-HGSIRSPIWRGGGIAHGPRGPTSYYYMLPMKVRVLGLKVALTVKLMQDDLHV
          RG..RKP..QK.SG..R..GSI.S.IW..G.IA.GP..P.SYYY.L.MKV....LKVAL.VKLMQD.LH.
Retrocopy RGSRRKP**QKVSGQDR<AGSIHSQIWQEGSIACGPQSPISYYYILSMKV*MFALKVALIVKLMQDELHM

Parental  VDSLELPTSDPKYLSDLVRHRCWGDSVLLVDVNEEMPQNIVSAVSNLKTINLI
          VD.LELP.SD..YL.DL.RHR...DSV.LVD..EE.PQN..SAVSNLK.I.L.
Retrocopy VDFLELPVSDTRYLLDLARHRV-RDSVVLVDIDEETPQNVISAVSNLKSISLV

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_633 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000008539	1 retrocopy	retro_shar_633 ,