RetrogeneDB ID: retro_ocun_176

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:43267131..43268043(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000013112
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMB5
• Ensembl ID: ENSOCUG00000013109
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 5 [Source:HGNC Symbol;Acc:9542]

Sequence

>retro_ocun_176
ATGGCTCTCCAGGAAGTGTGTGAGTGGCAGGCTCCTGACACCCAGGCGCTGGTGCCTCACCTGCCGCGGACTGGCAGCTG
GGCTGTGCCTAGGGGCTGCGATCCCCAAACCTTCCTGCAGACCCACGGCCCACAGCTGGCCCACGGCACCACCACCCTGG
CCTTCCGCTTCCGCCACGGGGTCATCGCCGCGGCTGACACGCGTTCTTCCTGTGGCAGCTACGTGGCCTGCCCAGCCTCA
CGCAAGATCATCCCCGTGCACCAGCACCTGCTGGGCACCACCTCGGGCACCTCTGCGGACTGTGTCACGTGGTACCGGGT
GCTACAGAGGGAGCTGCGGCTGCGGGCCCTGAGGGAGGGCCAACTGCCCAGTGTGGCCGGTGCAGCCAAGCTCTTGTCGG
TCATGCTGTCCCGCTACCGGGGGCTGGATCTGTGTGTGGCCACTGCCCTGTGTGGCTGGGACCGCTCTGGCCCTGCCCTC
TTCTACGTCTACAGCGATGGCACGTGGCTGCAGGGCGACATCTTCTCGGTAGGCTCGGGGTCTCCCTATGCCTACGGCGT
GCTAGACCGTGGCTACCGCTACGACATGGGCATCCAGGAGGCCTACGCCCTGGCTCGCTGCGCCGTGGCCCACGCCACCC
ACCGCGATGCCTACTCCGGGGGGTCTGTTGACCTTTTCCACGTGCGGGAGAGTGGATGGGAGTATGTGTCACGCAGTGAT
GCCTGTGTGCTGTACACGCAGCTGCAAAAACTCCCAGAGCCAGAGCCTGCAGAGGAGGAAGGGGAGGCCAGCCAGGCCCA
CCCTGAGCCTGCCACTCCCCACAGAGCTGGGGGAGGCAGGGGACTCTCTGCGGGGCCAGGGGAGGCGACACCAGGAGACT
TCAGGATGCCAGCAGAGACTGAGAGGCTGTGA

Alignment

ORF - retro_ocun_176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.71 %
• Parental protein coverage: 76.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIEMLHGTTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQC
          G....HGTTTLAF.FRHGVI.AAD.R...G.Y.A.....K.I.....LLGT..G..ADC..W.R.L.R..
Retrocopy GPQLAHGTTTLAFRFRHGVIAAADTRSSCGSYVACPASRKIIPVHQHLLGTTSGTSADCVTWYRVLQREL

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

Parental  YAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLH
          YAYGV.DRGY.YD.....AY.LAR.A...AT.RDAYSGG.V.L.HVRE.GW..VS......L.
Retrocopy YAYGVLDRGYRYDMGIQEAYALARCAVAHATHRDAYSGGSVDLFHVRESGWEYVSRSDACVLY

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.06 RPM	68.16 RPM
SRP017611_kidney	0.00 RPM	63.85 RPM
SRP017611_liver	0.00 RPM	30.68 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_176 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_176 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_95
Pan troglodytes	retro_ptro_97
Gorilla gorilla	retro_ggor_156
Pongo abelii	retro_pabe_171
Callithrix jacchus	retro_cjac_35
Bos taurus	retro_btau_11
Sus scrofa	retro_sscr_90
Canis familiaris	retro_cfam_75
Equus caballus	retro_ecab_18

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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,