RetrogeneDB ID: retro_meug_28

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_10133:2208..2913(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMEUG00000000835
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMB5
• Ensembl ID: ENSMEUG00000003572
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 5 [Source:HGNC Symbol;Acc:9542]

Sequence

>retro_meug_28
ATGGCTCTGGAGAATGTGTGCGATTGGCAGGCCCCTGAAGCCCTGAGCCCTCACCTACCTGGGGCTGGGGACTGGGCTGT
CCCCAGGGGCTGTGACCCTCCTGTCTTTCTGCAGACACACGGTCCAGAACTGGCCCATGGCACCACCACATTAGCCTTCC
GATTCCGCCACGGGGTCATTGCTGCAGCTGATACTCGATCTTCCTGTGGCTCCTACGTGGCTTGCCCTGCTTCCCAGAAG
GTCATCCCTGTCCACCAGCACCTTATAGGCACAACTTCAGGCACCTCAGCTGATTGTGCCACCTGGTACCGAATACTGCA
ACGGGAGCTGCGCCTTCGGGCTCTCAGGGAGGGCCAGCTGCCCAGTGTGGCAGGGGCTGCCAAGCTTCTCTCCACCATGC
TATACCGTTACCGGGGCTTGGACCTGTGTGTGGCCACAGCCCTGTGTGGCTGGGACCAGGCTGGCCCTGCCCTCTTTTAT
GTCTACAGTGATGGGACCCTCCTGGCCGGCGATGTCTTCTCTGTGGGCTCTGGCTCACCCTATGCCTATGGTGTGCTGGA
CCGTGGCTACCGCTATGACATGACTATTGAAGAGGCTTATACTCTGGCTCGCCAAGCTGTGGCCCATGCTACCCGCAGGG
ATGCCTATTCAGGTGGTTCTGTGGACCTGTACCATGTGAAGGAGAGTGGTTGGGAACGAGTGTCT

Alignment

ORF - retro_meug_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.67 %
• Parental protein coverage: 73.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIELLHGTTTLAFKFRHGVIVAVDSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQC
          G.EL.HGTTTLAF.FRHGVI.A.D.R...G.Y.A.....KVI.....L.GT..G..ADC..W.R.L.R..
Retrocopy GPELAHGTTTLAFRFRHGVIAAADTRSSCGSYVACPASQKVIPVHQHLIGTTSGTSADCATWYRILQREL

Parental  RIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGVTFSVGSGSV
          R...LR.....SVA.A.KLL..M.Y.Y.G..L...T..CGWD..GP.L.YV.S.G....G..FSVGSGS.
Retrocopy RLRALREGQLPSVAGAAKLLSTMLYRYRGLDLCVATALCGWDQAGPALFYVYSDGTLLAGDVFSVGSGSP

Parental  YAYGVMDQGYSFDLSVEEAYDLARRAIYQATYRDAYSGGVVNLYHVREDGWIRV
          YAYGV.D.GY..D...EEAY.LAR.A...AT.RDAYSGG.V.LYHV.E.GW.RV
Retrocopy YAYGVLDRGYRYDMTIEEAYTLARQAVAHATRRDAYSGGSVDLYHVKESGWERV

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_28 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_28 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634, retro_hsap_95,
Gorilla gorilla	ENSGGOG00000026856	2 retrocopies	retro_ggor_1232, retro_ggor_156,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28 ,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,