RetrogeneDB ID: retro_ocun_1040

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:46140641..46141075(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSOCUG00000006984
• Aliases: None
• Description: mitochondrial ribosomal protein S25 [Source:HGNC Symbol;Acc:14511]

Sequence

>retro_ocun_1040
GACTTGGTGAAAGTTATGATGGGGAATTACAACAGGCACCAGGAGCTGGGCTAGGGCACCAGGATGTTTGTTTTCAACAT
ACTTCAGATGCAGTACTAAAACCCCTGGATGCAGATCATGATGTTCAAGAACATGACGCTGTCGCCCTTCCTGCATTTCT
GTCCAGACTCTGGGGAGCAGGTCCTGGGGGATATGAGAACAAAGAGTAATGAGGAGATCATGGAGCAACATCTGAAGAAT
CTAGAGGAAGAATGAGGAAACCCTCAAGAAGGAGGAGCGGGAGAAAAACTCTCTCATCCAGCCAGCTTTGGCCCTCCAAA
GTCCTGCCTGTGCGAGTGCATCTGTGAGGTGGAAAGGCAGGTGCCCTGCCCAGGGCTGGTGCCATTACCCAAGGAGATGA
TAGGAAGTACAAAGCTCTGGAAGCCAGTGCCCAG

Alignment

ORF - retro_ocun_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 85.55 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DSVKVMTVNYNTRGELGEGARKFVFFNIPQIQYRNPWVQITMFKNMTPSPFLRFYLDSGEQVLVDMETKS
          D.VKVM..NYN...ELG.G.R.FVF.NI.Q.QY.NPW.QI.MFKNMT.SPFL.F..DSGEQVL.DM.TKS
Retrocopy DLVKVMMGNYNRHQELG*GTRMFVF-NILQMQY*NPWMQIMMFKNMTLSPFLHFCPDSGEQVLGDMRTKS

Parental  NKEIME-HIRRILGKNEETLKKEEQEKL-QLSHPANFGPRKYCLRECICEVEGQVPCPGLVPLPKEMTG-
          N.EIME..I.RI..KNEETL.K.E......LSHPA.FGP.K.CL.ECICEVE.QVPCPGLVPLPKEM.G.
Retrocopy NEEIME>NI*RI*RKNEETL-KKEEREK<KLSHPASFGPPKSCLCECICEVERQVPCPGLVPLPKEMIG<

Parental  KHKAALKASAQ
          K.K.AL.ASAQ
Retrocopy KYK-ALEASAQ

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	27.37 RPM
SRP017611_kidney	0.00 RPM	32.03 RPM
SRP017611_liver	0.00 RPM	8.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1040 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1040 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004349	1 retrocopy	retro_amel_1861,
Canis familiaris	ENSCAFG00000028683	1 retrocopy	retro_cfam_2200,
Echinops telfairi	ENSETEG00000008261	2 retrocopies	retro_etel_1144, retro_etel_1227,
Felis catus	ENSFCAG00000027687	1 retrocopy	retro_fcat_2014,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Loxodonta africana	ENSLAFG00000022178	1 retrocopy	retro_lafr_1068,
Mustela putorius furo	ENSMPUG00000017248	1 retrocopy	retro_mputfur_1608,
Oryctolagus cuniculus	ENSOCUG00000006984	1 retrocopy	retro_ocun_1040 ,
Ochotona princeps	ENSOPRG00000009370	3 retrocopies	retro_opri_288, retro_opri_690, retro_opri_951,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Tursiops truncatus	ENSTTRG00000009881	1 retrocopy	retro_ttru_140,