RetrogeneDB ID: retro_ocun_1029

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:22432092..22432594(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021170
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1029
GGTCCAGGCAGAGACCTGGGAGTGGACACCCACAGTGTCCTGGGCCATTGCAGCTGGCTTCACGCCTTAAGCCTCAAGGA
TGTACCGTATTGGCACTTGCTATAGCAGATTTCTCCGCTGTTGTTTCTGATTCTCGACTATTGAGCGAAGGATTTTCAGT
TCACACGAGGGACAGCCCTGGATGTTACACGTTAACAGTTAGAGCAGTCATCAGATGCAGCGGTTTTCACGGAGACTGTA
GGAACTTGAGAAAGATTTTTGAAGCCAGACTAAAGCTTTCCAATCAGGAGGTCATGGCCACAGGAGCAATTACTGAACTG
CTGTCTACACTCTACTCAAGACACTTCTTTCCATACTGTTTACAACATCCTCCGCAGACTGGAGGAAGAAGGGACGGGAG
TAGTGCACAGCTTTGACTCAGAGGAATCCTACCCGTGGGACTTCTTCAAGGCAGGAGGCTCTCCAGCGCCATCTGCAACG
CCTGGGAGACAACCAGGTTGGC

Alignment

ORF - retro_ocun_1029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.36 %
• Parental protein coverage: 71.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GPGRDLGMDVHSVA-GPVQRRFSPYAFNGGTVLAIAGEDFSIVASDTRL-SEGFSIHTRDSPKCYKLTDR
          GPGRDLG.D.HSV..GP.Q...S.....G.TVLA.A..DFS.V.SD.RL.SEGFS.HTRDSP.CY.LT.R
Retrocopy GPGRDLGVDTHSVL<GPLQLA-SRLKPQGCTVLALAIADFSAVVSDSRLLSEGFSVHTRDSPGCYTLTVR

Parental  TVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYY-VYNIIGGLDEEGK
          .VI.CSGFHGDC..L.KI.EARLK....SN...M.TGAI...LST.LYS.R.F..Y.VYNI...L.EEG.
Retrocopy AVIRCSGFHGDCRNLRKIFEARLKL---SNQEVMATGAITELLST-LYS-RHFFPY>VYNILRRLEEEGT

Parental  GAVYSFDPVGSYQRDSFKAGGS-ASAM-LQPLLDNQVG
          G.V.SFD...SY..D.FKAGGS..SA..LQ.L.DNQVG
Retrocopy GVVHSFDSEESYPWDFFKAGGS<SSAI<LQRLGDNQVG

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	0.00 RPM	63.58 RPM
SRP017611_kidney	0.00 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_1029 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1029 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1029 has 0 orthologous retrocopies within eutheria group .

---

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,