RetrogeneDB ID: retro_meug_2090

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold8891:10202..11111(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC6
• Ensembl ID: ENSMEUG00000007084
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 6 [Source:HGNC Symbol;Acc:9553]

Sequence

>retro_meug_2090
CTTCACAAGAGTAAGCGGAAGCCAGGGTCAAGAGTTGCTCTGGATATGACTACACTAACTATCACGAGATACTTGCCGAG
AGAAGTTGATCCTCTGGTTTACAACATGTCTCATGAAGATCCTGGGAATGTGTCTTATTCTGAGAATGGAGGGCTTTCTG
AACAAATCAGAGAATTAAGAGAGGTAATAGAATTACCCCTTAGAAACCCTGAATTATTCCAGCGTGTAGGAATAATACCT
CCAAAAAGTTGTTTGCTATATGGACCACCAGGAACAGGAAAAACACTCTTGGCAAGAGGTGTTGCTAGGCAGGTGGACTG
GAATTTTTTAAAGGTTGTATCCAGTTCCATTGTAGACAACTACATTGGTGAAATTGCTCATTTTATAAGAGAAATGTTCA
ATTATGCCAGGGATCACCAGCCATGCATCATTTTAATGGATGAAATAGATGCTATTGGTGGTTTTCGTTTTTCTGAGGGT
ACTTCAGCTGATAGAGAAATTCAGAGAACTCTAATGGAGTTACTGAATCAGATGGATGGATTTGATACTTTACACAGAGT
AAAAATGATCATGGCTACCAACAGACCAGACACATTGGATACTGCTTTGTTGTGTCCAGGAAGATGAGATAGAAAAATAC
ATATTGATTTACCAAATGAACAAGCAAGATAAGACATAATGAAGATTCATGCAAGTCCTATCACAAAACATGGTGAAATA
AATTGTGAAGCAATTGTGAAACTCTAAGATGGCTTTCATGGAGCAGATATAAGAAATGTTTACACTGAAGCAGGTATGTT
TGCAATTCTTGCTGATCACAATTTTGTAGTACAGGAAGATTTCATGAAGGCAGTAAGAAAAGTGGCTGATTCTAAGAAGT
TGGAATCTAAACTAGATTATAAATCTGTC

Alignment

ORF - retro_meug_2090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.13 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNP
          L.KSK.KPG.RVALDMTTLTI.RYLPREVDPLVYNMSHEDPGNVSYSE.GGLSEQIRELREVIELPL.NP
Retrocopy LHKSKRKPGSRVALDMTTLTITRYLPREVDPLVYNMSHEDPGNVSYSENGGLSEQIRELREVIELPLRNP

Parental  ELFQRVGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKV-SSSIVDKYIGESARLIREMFNYARDHQ
          ELFQRVGIIPPK.CLLYGPPGTGKTLLAR.VA.Q.D.NFLKV.SSSIVD.YIGE.A..IREMFNYARDHQ
Retrocopy ELFQRVGIIPPKSCLLYGPPGTGKTLLARGVARQVDWNFLKVVSSSIVDNYIGEIAHFIREMFNYARDHQ

Parental  PCIIFMDEIDAIXXXXXXXGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLDPALLRPGRLD
          PCII.MDEIDAI.......GTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLD.ALL.PGR.D
Retrocopy PCIILMDEIDAIGGFRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLDTALLCPGR*D

Parental  RKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHDFVVQED
          RKIHIDLPNEQAR.DI.KIHA.PITKHGEI..EAIVKL.DGF.GAD.RNV.TEAGMFAI.ADH.FVVQED
Retrocopy RKIHIDLPNEQAR*DIMKIHASPITKHGEINCEAIVKL*DGFHGADIRNVYTEAGMFAILADHNFVVQED

Parental  FMKAVRKVADSKKLESKLDYKPV
          FMKAVRKVADSKKLESKLDYK.V
Retrocopy FMKAVRKVADSKKLESKLDYKSV

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_2090 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2090 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007126	2 retrocopies	retro_cjac_204, retro_cjac_3221,
Cavia porcellus	ENSCPOG00000009477	1 retrocopy	retro_cpor_47,
Homo sapiens	ENSG00000100519	2 retrocopies	retro_hsap_1022, retro_hsap_4059,
Gorilla gorilla	ENSGGOG00000002152	2 retrocopies	retro_ggor_2727, retro_ggor_808,
Macropus eugenii	ENSMEUG00000007084	3 retrocopies	retro_meug_1700, retro_meug_2090 , retro_meug_923,
Monodelphis domestica	ENSMODG00000014500	1 retrocopy	retro_mdom_438,
Nomascus leucogenys	ENSNLEG00000012518	2 retrocopies	retro_nleu_559, retro_nleu_900,
Otolemur garnettii	ENSOGAG00000010011	1 retrocopy	retro_ogar_3101,
Pongo abelii	ENSPPYG00000005820	2 retrocopies	retro_pabe_3334, retro_pabe_858,
Pan troglodytes	ENSPTRG00000006352	2 retrocopies	retro_ptro_2752, retro_ptro_699,
Rattus norvegicus	ENSRNOG00000007203	1 retrocopy	retro_rnor_1480,
Tursiops truncatus	ENSTTRG00000003880	1 retrocopy	retro_ttru_117,