RetrogeneDB ID: retro_shar_520

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849764.1:4088474..4089012(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000006005
• Aliases: None
• Description: None

Sequence

>retro_shar_520
ATTATCAGCGATTCTGTGGATTTGTGTGATGCTTGGGAGGCCACGGAAGAATATTAGGATATAGACCACATAAGTCCATT
GGAGTGTCCAACTTCAACTGCAGGCAATTGGAGATGATATTGAATAAAGCTGGAATTAAATAGGAACCTGTCTGTAATCA
GATGCAACATCATCCTTACCTGAATGACAGCAAATTGTTGGAGTTCTGCAAGTCAAATGCTGTCCTATTGGTAACAAACA
GTGCTTTGGATCCCACAGAGTAGATGAAAAGATTCCCATTCTCCTAGGTGACTCAGTCCTGGGAGCCATTGCCAAGAATC
ACAATTGGATTTCAGCCCAGGTTATTTCCCGATATCAGATTCAGTGAGGGGTGGTAGTCTTAACAAAGAGCTGGATCAAA
GAGAACTTTCAGTTGTTTGATTTCCAATTGACTCCAGAAGACATGGAAGTTACTTTTAGTCTTAAGAAAAACTTCCCCTG
TCTCACCCTTCCTTGCTCAATTCAAGGAAAGCAGCAACTATCCTTTAATGATGAATAT

Alignment

ORF - retro_shar_520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IIFEFVDLRDTWEAMEKCKDAGLV-KSIGVSNFNRRQLEMILNKTGLKYKPVCNQVECHPYLNQSKLLEF
          II...VDL.D.WEA.E...D.....KSIGVSNFN.RQLEMILNK.G.K..PVCNQ...HPYLN.SKLLEF
Retrocopy IISDSVDLCDAWEATEEY*DIDHI<KSIGVSNFNCRQLEMILNKAGIK*EPVCNQMQHHPYLNDSKLLEF

Parental  CKSNDIILVAYSAL-GSNRESPWIDEKSPVLLDDPVLGTIAKKHNRSPAQVALRYQIQRGVVVLAKSFSE
          CKSN...LV..SAL.GS.R.....DEK.P.LL.D.VLG.IAK.HN...AQV..RYQIQ.GVVVL.KS...
Retrocopy CKSNAVLLVTNSAL<GSHR----VDEKIPILLGDSVLGAIAKNHNWISAQVISRYQIQ*GVVVLTKSW--

Parental  KRIKENFQVFDFQLTSEDMKVIDGLNRNLRYLTLDI-FQDNINYPFNDDY
          ..IKENFQ.FDFQLT.EDM.V...L..N...LTL....Q......FND.Y
Retrocopy --IKENFQLFDFQLTPEDMEVTFSLKKNFPCLTLPCSIQGKQQLSFNDEY

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_520 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008668	1 retrocopy	retro_chof_568,
Echinops telfairi	ENSETEG00000009155	1 retrocopy	retro_etel_352,
Rattus norvegicus	ENSRNOG00000038361	1 retrocopy	retro_rnor_2046,
Sarcophilus harrisii	ENSSHAG00000006005	1 retrocopy	retro_shar_520 ,