RetrogeneDB ID: retro_meug_173

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_5101:84502..85347(-)
• Located in intron of: ENSMEUG00000011296

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSMEUG00000006596
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_meug_173
GCAGCAGCAGCGAATGAGGCCACCAGGGTGAGCAGTGCTGGGGACCCGGGGGTGGTCGTGCAGGTGGCAGCCAGCATGTA
CGAGCAGCTCAAGGGCGAGTGGAACGGCCAAGAGCCCCAGTCTGAGCAAGTGTGGTGAGGAGCTGGGCCGCCTCAAGCTG
GTTTTGCTGGAGTTCAACTTCCTGCCTACTACCGGTACAAAACTGACCCAACAGCAGCTTATCCTGGCCTATGACTTCTT
GGAGATTGGTGCCCCATGGAGCATTCTGCGGAAGGACATACCCTCCTTTGAGTGATACATGGCTCAGCTTTAAATGTTAT
TACTTTGACTACAAGTTGCAGCTCCCCGAGTCGGCCTACATGCACCAGTTTCTGGGCCTCAGTCTACTCTTCTTGCTGTC
CCAGAACCTAGTGGCCGAGTCCCACATTGAGCTGAAGCAGCTCCCTGCTAAGGACATCCAGACCAATGTCTACATCAAGC
ACCCTGTGTCCTTAGAGCAGTACCTGATGGAAGGAAGCTACAATAAGTAGTTCCTGGCCAAGGGAAATATCCCTGCTGAG
AGCTACACGTTCTTCATTGACATTTTGCTAGATACGATAAGGGATAAGATTGACGGATGCATTGAGAAGGCCTATGAAAA
GATCCTGCTTGCGGGAGCCACGAGAATTTTCTTCACCACCCCCAAGAAGATGACTGAGTACGCCAAGAAGAGAGGGTGAG
TCCTGGGCCCCAGCAATTACCACAGCTTCAAGTGCCAGCAGCAGAAGCCTGAGGATACCACCATCCCCTCCACAGAGCTG
ACAAAGCAAGTCATCAAGTATGCAAGGCAGCTGGAGATGATTGTC

Alignment

ORF - retro_meug_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 92.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAAANGAAGVSGAGAPAVL-QAAAGMYEQLKGEWN-RKSPNLSKCGEELGRLKLVLLELNFLPTTGTKLT
          AAAAN.A..VS.AG.P.V..Q.AA.MYEQLKGEWN..KSP.LSKCGEELGRLKLVLLE.NFLPTTGTKLT
Retrocopy AAAANEATRVSSAGDPGVVVQVAASMYEQLKGEWN>AKSPSLSKCGEELGRLKLVLLEFNFLPTTGTKLT

Parental  KQQLILARDILEIGAQWSILRKDIPSFERYMAQL-KCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRVA
          .QQLILA.D.LEIGA.WSILRKDIPSFE.YMAQL.KCYYFDYK.QLPESAYMHQ.LGL.LLFLLSQN.VA
Retrocopy QQQLILAYDFLEIGAPWSILRKDIPSFE*YMAQL>KCYYFDYKLQLPESAYMHQFLGLSLLFLLSQNLVA

Parental  EFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIE
          E.H.EL..LPAKDIQTNVYIKHPVSLEQYLMEGSYNK.FLAKGNIPAESYTFFIDILLDTIRD.I.GCIE
Retrocopy ESHIELKQLPAKDIQTNVYIKHPVSLEQYLMEGSYNK*FLAKGNIPAESYTFFIDILLDTIRDKIDGCIE

Parental  KAYEKILFAEATRILFFTTPKKMTEYAKKRGWVLGPSNYYSFKCQQQKPEDTTIPSTELAKQVIEYARQL
          KAYEKIL.A.ATRI.FFTTPKKMTEYAKKRG.VLGPSNY.SFKCQQQKPEDTTIPSTEL.KQVI.YARQL
Retrocopy KAYEKILLAGATRI-FFTTPKKMTEYAKKRG*VLGPSNYHSFKCQQQKPEDTTIPSTELTKQVIKYARQL

Parental  EMIV
          EMIV
Retrocopy EMIV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_173 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_173 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006596	2 retrocopies	retro_meug_1494, retro_meug_173 ,
Macaca mulatta	ENSMMUG00000031219	1 retrocopy	retro_mmul_534,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,