RetrogeneDB ID: retro_shar_496

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849686.1:2117885..2118376(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDDC1
• Ensembl ID: ENSSHAG00000003122
• Aliases: None
• Description: Parkinson disease 7 domain containing 1 [Source:HGNC Symbol;Acc:26616]

Sequence

>retro_shar_496
GACTTTGTGGTATGAGCAAAAGTAATAACCGTTGGATCCAGGACTTCACATGAAGACCCATACCAGCCTAACCAAATTGG
AGTCTATTGACAATGCAAGGTACCACGCCCTGCTCAGCCCCAGCTCCCCCAAGGCACTAGGTGACCTTGACAATAGGACA
TACAAGCCTGTATCTTTGAGCATTTCAGCATTGAGCAAAAGTCCATTTGTGCCATGGGACAAGACATAGACATTTTCTGT
TGTGCTGCTAAGAAAAGAAAACAAATATTTCAGGATTGCAATCTGAATGGCTGACTGTGTGCTAGATCATCTGGCAGCCT
AGCCCTAGGACCCTACCCATCATCACAGAAGACTCGTGAAAGCCCAGCCACAGTGCCAGCTGGCCAGATGCTGTGCATGT
TGTCCAGGATTGACACTTGGTCAGAGGCCAGAATAACACCTCCACAGTCCTAATTGTGCAAAATTTGCTGCTCTTGTGTA
GAGGCAGAAAG

Alignment

ORF - retro_shar_496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.4 %
• Parental protein coverage: 77.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DFV-GVNESNMRWIQDF-RMKAYASPAKLESIDGARYHALLIPSCPGALTDLANSGYL-ARILEHFSTEQ
          DFV.G...SN.RWIQDF..MK...S..KLESID.ARYHALL.PS.P.AL.DL.N..Y..A.I.EHFS.EQ
Retrocopy DFV<GMSKSNNRWIQDF<HMKTHTSLTKLESIDNARYHALLSPSSPKALGDLDNRTYK<ACIFEHFSIEQ

Parental  KPICAVGHGVAALCCATEDKAWVFQNYSLTG-PPVCELVRQPGFGSLPIIMEDFVKDAGACFSASQPDAV
          K.ICA.G......CCA.......FQ...L.G...VC....QP....LPII.ED..K......SAS.PDAV
Retrocopy KSICAMGQDIDIFCCAAKKRKQIFQDCNLNG<LTVC*IIWQPSPRTLPIITEDS*KPS---HSASWPDAV

Parental  HVVLDRHLVTGQNEASTVLAVQNLVFLCGSRK
          HVV.D.HLV.GQN..STVL.VQNL..LC..RK
Retrocopy HVVQD*HLVRGQNNTSTVLIVQNLLLLCRGRK

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_496 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000005033	1 retrocopy	retro_meug_954,
Myotis lucifugus	ENSMLUG00000017584	1 retrocopy	retro_mluc_2267,
Mus musculus	ENSMUSG00000051007	1 retrocopy	retro_mmus_2040,
Rattus norvegicus	ENSRNOG00000046382	1 retrocopy	retro_rnor_1887,
Sarcophilus harrisii	ENSSHAG00000003122	1 retrocopy	retro_shar_496 ,