RetrogeneDB ID: retro_shar_403

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841599.1:1289538..1290098(+)
• Located in intron of: ENSSHAG00000013122

Retrocopy information

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

Parental gene information

• Parental gene symbol: POR
• Ensembl ID: ENSSHAG00000013704
• Aliases: None
• Description: P450 (cytochrome) oxidoreductase [Source:HGNC Symbol;Acc:9208]

Sequence

>retro_shar_403
ATTTCCCAACCCTCTTTCCTCAGCAACATTTGTGGACTCTTCATTGACTTTATTCATGGTCTTGGTTACTGTTTATGCCT
TGATCTCTCTGAATCAGTTGCATGAAATTAGATCAGAAATTCCCTTTCAGTCTGTTGAGGTGGGCCATGATGCTCAACTG
TATTTCAGGATCTTCAGTTGAAAGAAGAGGTATCCAGACCAGGAAGATTAATCCAGTCCCAGGATACTACCTTACAGAGA
ATTATCATTCTTACCCCATGCCGACCCTCCAGATCATTCAGATGCAGCAACATGACAACAGCCAGAGATTGGCATCCTGG
CTAAACAATGAACCTAGGAACCCACCTACCCCACTTCCCTATCACCCAGCTTCTGGCCAGTTTTATGTGCAGACCCCTTT
TGGCTTTGTTCCTGCCTCCTCTAACTTCTACCCCACTGTCTCCTGCCCTTCCCAGGGAAGGAGCCTCCCACAGCCTCCAG
TCTGACAAGGGCCAGGGCACCCGACCCCGGGTGACAGCGTAACCTCAGTACCCATGGAGGTGTCCAGGGTCCAGATGCAA

Alignment

ORF - retro_shar_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 60.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IPQTSFLSNICGLFIGFIYGLGYCSCLDLSESVA-LKLDHKFPFSLLRRATVLNYVSGSSLERRAIQTRK
          I.Q.SFLSNICGLFI.FI.GLGYC.CLDLSESVA..KLD.KFPFSLLR.A..LN..SGSS.ERR.IQTRK
Retrocopy ISQPSFLSNICGLFIDFIHGLGYCLCLDLSESVA<MKLDQKFPFSLLRWAMMLNCISGSSVERRGIQTRK

Parental  INPVPGSYPTQNYHSYPMPTLQVIQMQQHDNSQRLASWPNNEPRSPPAPPPYHPASGQFYVQNPFGFAPA
          INPVPG.Y.T.NYHSYPMPTLQ.IQMQQHDNSQRLASW.NNEPR.PP.P.PYHPASGQFYVQ.PFGF.PA
Retrocopy INPVPGYYLTENYHSYPMPTLQIIQMQQHDNSQRLASWLNNEPRNPPTPLPYHPASGQFYVQTPFGFVPA

Parental  SSNFYPAVSCPSQGSCPPQPPVCQGPGQPTLGDSAISAPTEGSRVQRQ
          SSNFYP.VSCPSQG...PQPPV.QGPG.PT.GDS..S.P.E.SRVQ.Q
Retrocopy SSNFYPTVSCPSQGRSLPQPPV*QGPGHPTPGDSVTSVPMEVSRVQMQ

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_403 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	ENSSHAG00000013704	1 retrocopy	retro_shar_403 ,