RetrogeneDB ID: retro_meug_1052

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold27046:29902..30544(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME1
• Ensembl ID: ENSMEUG00000014712
• Aliases: None
• Description: proteasome (prosome, macropain) activator subunit 1 (PA28 alpha) [Source:HGNC Symbol;Acc:9568]

Sequence

>retro_meug_1052
ACCCTCAGTGTCAGACCTGAAGCCCAAGTCGAGGTAGATTTGTTTCGAAAGGAGTTAGGTGTTCATGCAGACAGTATACT
TGGAACCCTATTTTTCTGTGAAGATTTCGGAGCTGAAGGACCCATCTCTGAATGAGGCCAATTTGAGTCTCCTCAAGGGC
TCCCTGGACACTTCAGTCCCTGAACCAGCCAAAGCAAAAGAGAAGGAAGAGTGCTGGAAACCAGAAGAGAAGGATGATAA
GGATGGAAAGAAAAAACAGAGAGATGAAGATAAAAGTCCTCCTTGTGGGCCTGTAAGTTGCATTGAGAAGATCATGACCC
TTCTGGGGCAGCTGAAACCTGAGATCAAAGATGTGAAAGAACAGCTTAACCTGGTTTCCATGGACTGCAGTTACAGGTGC
CCTGAACTGAGAATGGGAACAGCTTTGGAGTAGCTGTCCAGGAGAAGGTATTTGAGCTGATGACTAATGCTCAGAACTAT
GCTGGTGGCTTCCAAACCCATATCTCAAAGTACTCTCTGAAAGGAGTGGCTAAAGTAGCAAAGCAGTCAAGTGTGGTTGG
CTACCGACAGCTGGTTCAGGAATTGGATAAAGCACAGTATGGAGAGACAAGGCTGAAGGTCATGGAGATCTGAAATACTT
AT

Alignment

ORF - retro_meug_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.4 %
• Parental protein coverage: 88.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TFSVRPEAQAKVDVFRKELCAQAEILLGT-YFPVKVSELDEFLKDPSLNEADLSLLKAALDIPIPDPAKE
          T.SVRPEAQ..VD.FRKEL...A...LGT.YF.VK.SE....LKDPSLNEA.LSLLK..LD...P.PAK.
Retrocopy TLSVRPEAQVEVDLFRKELGVHADSILGT>YFSVKISE----LKDPSLNEANLSLLKGSLDTSVPEPAKA

Parental  KEKEERRKQEEKEEKDGKKKEEDEDKGPPCGPVSCNEKIVALLGRLKPEIKDVKEQLNVVSM-WLQLQVP
          KEKEE..K.EEK..KDGKKK..DEDK.PPCGPVSC.EKI..LLG.LKPEIKDVKEQLN.VSM..LQLQVP
Retrocopy KEKEECWKPEEKDDKDGKKKQRDEDKSPPCGPVSCIEKIMTLLGQLKPEIKDVKEQLNLVSM<GLQLQVP

Parental  RIEDGNNFGVAVQEKVFELMTTLRTKLDGFQTQISKYFSERGDAVAKAAKQPHVGDYRQLVHELDEAQYG
          ..E.GN.FGVAVQEKVFELMT.......GFQT.ISKY.S..G..VAK.AKQ..V..YRQLV.ELD.AQYG
Retrocopy *TENGNSFGVAVQEKVFELMTNAQNYAGGFQTHISKY-SLKG--VAKVAKQSSVVGYRQLVQELDKAQYG

Parental  ETRLMVMEIRNTY
          ETRL.VMEI.NTY
Retrocopy ETRLKVMEI*NTY

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_1052 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1052 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016433	1 retrocopy	retro_amel_637,
Bos taurus	ENSBTAG00000021395	1 retrocopy	retro_btau_1189,
Canis familiaris	ENSCAFG00000011924	1 retrocopy	retro_cfam_246,
Equus caballus	ENSECAG00000016855	1 retrocopy	retro_ecab_1001,
Felis catus	ENSFCAG00000005583	1 retrocopy	retro_fcat_1567,
Macropus eugenii	ENSMEUG00000014712	1 retrocopy	retro_meug_1052 ,
Mus musculus	ENSMUSG00000022216	1 retrocopy	retro_mmus_466,
Rattus norvegicus	ENSRNOG00000019041	1 retrocopy	retro_rnor_50,
Tursiops truncatus	ENSTTRG00000008620	1 retrocopy	retro_ttru_569,