RetrogeneDB ID: retro_ocun_1448

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:40741789..40742372(-)
• Located in intron of: ENSOCUG00000010087

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMG2
• Ensembl ID: ENSOCUG00000005086
• Aliases: None
• Description: proteasome (prosome, macropain) assembly chaperone 2 [Source:HGNC Symbol;Acc:24929]

Sequence

>retro_ocun_1448
AATGTGAGCCAGTTTGCAATAGGTCTGATCATTTCTACCCTGATTATGTTTGCAATCAGTTACTTCTATACTGACTGTCA
CATGCCAATGATTGGAAACAACCCCTATGCAACAGTGGAAGAAAATGCAACCAAACTCAGTACAAATGCAGAAGTATATT
CATTGCTTCCAAAGGAGCTAGCGGCTCTTCAGTTAAACTCCGTTTTTACAAGGTATAAATCTAAGTCATTCTGTGAAAAA
CTGCTTTCCTGGGTGAAAAGTGGTAGCTGTGTTAGGGTTACTGTTCCTCCCGACAGTCATTTCCTATCACTTCCTAGTGA
TAAACAGCTCTGCAACACCCCATCCCAGGACCTACATACACCTTCCATGCAAAAAAAAAAAAAATGTGTTCAAGATAAAA
TAAAGAGTCTTAAGTGGCACAATATGGGAAAACACCCATGTGTTCCTGCAAAGGAGGAGTCTGAGCTTGGCATGTGTCCT
GGGAGAGGGCATCACAAAAGCACTGTATGATGGCAGCTGTTCTAAAGAGACCCAAGTGGCACTTCTGCCGAAATTTGCCT
CAGAAGGGGACAGCCCTGATGCA

Alignment

ORF - retro_ocun_1448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.42 %
• Parental protein coverage: 51.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVGQLAIDLIISTLDMCKIGYFYTDCLVPIVGNNPYATANENAAELSTNAEVYSLPSKKLVVLQLRSIFI
          NV.Q.AI.LIISTL.M..I.YFYTDC..P..GNNPYAT..ENA..LSTNAEVYSL..K.L..LQL.S.F.
Retrocopy NVSQFAIGLIISTLIMFAISYFYTDCHMPMIGNNPYATVEENATKLSTNAEVYSLLPKELAALQLNSVFT

Parental  KYKSKSFCEKLLCWVENSGCTRVIVLSSSHSYHR-NDKQLCSTPFRYLLTPSMQK---TVQNKIKSLNWQ
          .YKSKSFCEKLL.WV....C.RV.V...SH......DKQLC.TP...L.TPSMQK....VQ.KIKSL.W.
Retrocopy RYKSKSFCEKLLSWVKSGSCVRVTVPPDSHFLSLPSDKQLCNTPSQDLHTPSMQKKKKCVQDKIKSLKWH

Parental  EMEKSPCIPEIEDSDLCVRVPG-GGITKLLYDESCSKDIQMAVLLKFVSEGDNIPDA
          .M.K.PC.P..E.S.L....PG..GITK.LYD.SCSK..Q.A.L.KF.SEGD..PDA
Retrocopy NMGKHPCVPAKEESELGM-CPG>EGITKALYDGSCSKETQVALLPKFASEGDS-PDA

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	12.03 RPM
SRP017611_kidney	0.00 RPM	17.03 RPM
SRP017611_liver	0.00 RPM	5.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1448 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1448 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018855	1 retrocopy	retro_cfam_424,
Choloepus hoffmanni	ENSCHOG00000010042	1 retrocopy	retro_chof_1738,
Myotis lucifugus	ENSMLUG00000017744	1 retrocopy	retro_mluc_2496,
Macaca mulatta	ENSMMUG00000021855	1 retrocopy	retro_mmul_198,
Nomascus leucogenys	ENSNLEG00000009063	1 retrocopy	retro_nleu_1753,
Oryctolagus cuniculus	ENSOCUG00000005086	1 retrocopy	retro_ocun_1448 ,
Sus scrofa	ENSSSCG00000021827	2 retrocopies	retro_sscr_1008, retro_sscr_763,