RetrogeneDB ID: retro_ocun_620

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:93061494..93061957(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB1
• Ensembl ID: ENSOCUG00000007973
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 1 [Source:HGNC Symbol;Acc:9537]

Sequence

>retro_ocun_620
GGAGACTGTCTTACCTTGACAAAGATTATTGAAGCATGACTAAAGATGTATAAGCATTCCAATAATAAGGCCATGACTAC
AGGGGCAATTGCTGCAATGCTGTCTACAATCCTGTACTCCAGGCGCTTCTTTCCATACTATGTTTACAACATCATCGGTG
GACTTGATGAAGAAGGGAAGGGAGCCGTACAGCTTTGACGCAGTGGGATCCTACCAGCGAGACTCCTTCAAGGCTGGAGG
ATCTGCCAGTGCCATGCTGCAACCCCTGCTGGACAACCAGGTTGGCTTTAAGAACATGCAGAACGTTGAGCACATCCCAC
TGACCTTGGACAGAGCCACGCGACTGGTGAAAGATGTCTTCATTTATGCAGCCGAGAGGGACGTGTATACAGGGGACGCA
CTCCGGATCTGCATTGTAACCAAAGAAGGCATCAGGGAGGAGACTGTCCCCCTGCGGAAGGAC

Alignment

ORF - retro_ocun_620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 64.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGG-LDEEGKGAVYSFDPV
          GDCLTLTKIIEA.LKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGG.L...G....YSFD.V
Retrocopy GDCLTLTKIIEA*LKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGG>LMKKGREP-YSFDAV

Parental  GSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHIPLTLDRAMRLVKDVFISAAERDVYTGDALRICI
          GSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHIPLTLDRA.RLVKDVFI.AAERDVYTGDALRICI
Retrocopy GSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHIPLTLDRATRLVKDVFIYAAERDVYTGDALRICI

Parental  VTKEGIREETVPLRKD
          VTKEGIREETVPLRKD
Retrocopy VTKEGIREETVPLRKD

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	0.11 RPM	63.58 RPM
SRP017611_kidney	0.10 RPM	62.03 RPM
SRP017611_liver	0.00 RPM	37.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_620 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_620 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_620 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620 ,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,