RetrogeneDB ID: retro_ocun_609

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:45678146..45678695(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS7
• Ensembl ID: ENSOCUG00000017928
• Aliases: None
• Description: mitochondrial ribosomal protein S7 [Source:HGNC Symbol;Acc:14499]

Sequence

>retro_ocun_609
TGGATATTGGAGCTCATGCAGGTGAGTTGGAGCATGCATGGTCCTGAGTATAGGGATCCCTGTGTTGAGAAGGAGCATTA
CTGCAAGCCAATGGCCAGCTCCCTTAGGAGGAGAAATACTTTTCATGAGCTCAAGAAAACTCAGCTCATCAAAGCTGTGC
CAGCCACAAAAACAAGCTCTGTTTTTGATGACTTGGTGACCAGTAAATTCACCAGCATGATGATGAAAGGAGGAAACAAA
GTCCTGGCCAGATCCCTGATGACGCAGACTCTGGAAGCTATGAAGAGGAAGCAATTTGAGAAGTACCACGCTGCCTCTGC
AGAAAAAAAAGCAACCATAGAGCACAACCCTATGTCATCTTTCACCAAGCACTGAGAAACGGTGAGCCTTTGATTGGGCT
GGTACCCAGCCTCAGGGGTGGGCATTTCCTCCAGGTCCCTGTGCTGCTGGCTGACTGACGATGCCACTTCCTGGCCATGA
AATGGATGATCACTGCGTGTTGTGAGAAGCAGCACTGGGCGGATGCTGATGCTGGAGAAGCTGCCACAT

Alignment

ORF - retro_ocun_609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.35 %
• Parental protein coverage: 75.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WLPGLTQVRWSRYGPEYRDPRVEKEHYRKPAAELTEEERYDRELRKTQLIKAAPATTTGSVFEDPVISKF
          W...L.QV.WS..GPEYRDP.VEKEHY.KP.A..........EL.KTQLIKA.PAT.T.SVF.D.V.SKF
Retrocopy WILELMQVSWSMHGPEYRDPCVEKEHYCKPMASSLRRRNTFHELKKTQLIKAVPATKTSSVFDDLVTSKF

Parental  TNMMMKGGNKVLARSLMTQTLEAVKRKQFEKYQAASAEEQATIERN-PYVIFHQALKNCEPVIGLVPILR
          T.MMMKGGNKVLARSLMTQTLEA.KRKQFEKY.AASAE..ATIE.N.PYVIFHQAL.N.EP.IGLVP.LR
Retrocopy TSMMMKGGNKVLARSLMTQTLEAMKRKQFEKYHAASAEKKATIEHN<PYVIFHQALRNGEPLIGLVPSLR

Parental  GGHFYQVPVPLAERRRRFLAMKWMITECREKKQ-RRTLMPEKLSH
          GGHF.QVPV.LA..R..FLAMKWMIT.C.EK....R.LM.EKL.H
Retrocopy GGHFLQVPVLLAD*RCHFLAMKWMITACCEKQH>GRMLMLEKLPH

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	5.02 RPM
SRP017611_kidney	0.00 RPM	6.49 RPM
SRP017611_liver	0.00 RPM	1.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_609 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_609 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009287	1 retrocopy	retro_amel_1444,
Canis familiaris	ENSCAFG00000004752	5 retrocopies	retro_cfam_2020, retro_cfam_2197, retro_cfam_438, retro_cfam_443, retro_cfam_540,
Callithrix jacchus	ENSCJAG00000014458	2 retrocopies	retro_cjac_290, retro_cjac_3316,
Felis catus	ENSFCAG00000028759	2 retrocopies	retro_fcat_2013, retro_fcat_424,
Loxodonta africana	ENSLAFG00000002873	1 retrocopy	retro_lafr_945,
Macropus eugenii	ENSMEUG00000012264	1 retrocopy	retro_meug_1826,
Mustela putorius furo	ENSMPUG00000013928	1 retrocopy	retro_mputfur_976,
Oryctolagus cuniculus	ENSOCUG00000017928	1 retrocopy	retro_ocun_609 ,
Procavia capensis	ENSPCAG00000015942	1 retrocopy	retro_pcap_327,
Pteropus vampyrus	ENSPVAG00000008433	3 retrocopies	retro_pvam_610, retro_pvam_615, retro_pvam_678,