RetrogeneDB ID: retro_shar_199

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834626.1:797219..797600(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPX3
• Ensembl ID: ENSSHAG00000001286
• Aliases: None
• Description: glutathione peroxidase 3 (plasma) [Source:HGNC Symbol;Acc:4555]

Sequence

>retro_shar_199
GACCTCTGCCCAGGGATTACAGGTACCATCATGATTATGGGGCCCTCACCATTAATGGTGATGAATACATCCCTTTCAAG
CAATATGCAGGCAAATCTGTCTTCCCTGTCACTTGTTGCCACCTACTGAGACCAAACGGTCCAGTACCATGAACTGAACA
GACTACTGGAAGACCTGAAGTCCCCGAACCTTGTTATACTGGATTCACCGCCAATCAATTTGGAAAACAAGAACCAGGAC
AGAACTCAGAAATCCCCGCTGCTCTCAAATACGTGCGCCCAGTTGGAGCTTTCTGCTCAGTTTCCAGCAATTTGAGAAAG
AACATGTGAATGGGGAGAAAGAACAGACGTTTCCACGTTTCTGAAGAATCCCTGCCCTCCT

Alignment

ORF - retro_shar_199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.92 %
• Parental protein coverage: 57.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DCYQGITGNI-YDYGALTIDTDEYIPFKQYAGKYVLFVN-VATYHGFLEGWSELNALQEDLKSQNLVIL-
          D...GITG.I..DYGALTI..DEYIPFKQYAGK.V..V..VATY........ELN.L.EDLKS.NLVIL.
Retrocopy DLCPGITGTI<HDYGALTINGDEYIPFKQYAGKSVFPVT>VATY*DQTVQYHELNRLLEDLKSPNLVIL<

Parental  GFPCNQFGKQEPGQNSEVLPALKHVRPGG-GFVPNFQLFEKGDVNGEKEQ-KVYTFLKNSCPP
          GF..NQFGKQEPGQNSE...ALK.VRP.G..F...FQ.FEK..VNGEKEQ..V.TFLKN.CPP
Retrocopy GFTANQFGKQEPGQNSEIPAALKYVRPVG<SFLLSFQQFEKEHVNGEKEQ<DVSTFLKNPCPP

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_199 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000000660	1 retrocopy	retro_mmur_740,
Sarcophilus harrisii	ENSSHAG00000001286	1 retrocopy	retro_shar_199 ,