RetrogeneDB ID: retro_ocun_1747

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018842:13571..14032(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS31
• Ensembl ID: ENSOCUG00000021467
• Aliases: None
• Description: mitochondrial ribosomal protein S31 [Source:HGNC Symbol;Acc:16632]

Sequence

>retro_ocun_1747
CAGACCACAAAGCCACCCAAGCGAAGGGCTCTGGAAGGTGAGGAGGCTGTCATTGGCAAGCTTCAAAGAGCTAAAAGGAC
GGCCCAAAGACGAGAGAGAAGCCTCCGAGCCCCGAGTTGGTGGCAGCTGCGACTGCTGTGGCAGATTCTCTCCCTTTGAC
CAGCAGAGCCCCAGGCACACCTGCTCAGGCAGCTCCAGCACACGAGGAAGCCCCGTGGGCACAGGGGGACCGGCCGAGGC
CTAAGGTCAGTCTCAGGAGCATCACATCAGATATGAAAGCTGCCAGGCCTGCGGCAGCCGGGGTTCATACACGACCAGAG
CCTCAGATTCAGTCTGACGAAGGATCTGAGGTCCTCTGGACAGAAGACTGCTGATCTCAGAAAATTATTAGGACAAACGT
ATTCAAGGGGGAGAGGCTTGATATTTTGGACCCTAAGACACTCACTGGAGAAGCACCTGAA

Alignment

ORF - retro_ocun_1747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.75 %
• Parental protein coverage: 59.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QTTKPPNRRLLEGEEAVIGKLQRAK-KDGPKKRDKPLSPELVAAATAVADSLPFDKQKTKSDPLRQLPAA
          QTTKPP.RR.LEGEEAVIGKLQRAK.KDGPK.R.KP.SPELVAAATAVADSLP.........P....PA.
Retrocopy QTTKPPKRRALEGEEAVIGKLQRAK<KDGPKTREKPPSPELVAAATAVADSLPL-TSRAPGTPAQAAPAH

Parental  MRKPRGTEEAKRKHFSFRNIISDMKVARPATARVHIRPEHQIQFDEGSD-SSLDQ-KTTDLR-KSIRKNL
          ...P.......R...S.R.I.SDMK.ARPA.A.VH.RPE.QIQ.DEGS....LD..KT.DLR.K.IR.N.
Retrocopy EEAPWAQGDRPRPKVSLRSITSDMKAARPAAAGVHTRPEPQIQSDEGSE<GPLDR<KTADLR<KIIRTNV

Parental  FKGKRLNIFDSKTLTEEAPE
          FKG.RL.I.D.KTLT.EAPE
Retrocopy FKGERLDILDPKTLTGEAPE

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	0.28 RPM	7.73 RPM
SRP017611_kidney	0.00 RPM	6.89 RPM
SRP017611_liver	0.00 RPM	5.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1747 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1747 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008470	1 retrocopy	retro_chof_586,
Equus caballus	ENSECAG00000003600	1 retrocopy	retro_ecab_1028,
Nomascus leucogenys	ENSNLEG00000001164	1 retrocopy	retro_nleu_1999,
Oryctolagus cuniculus	ENSOCUG00000021467	1 retrocopy	retro_ocun_1747 ,
Otolemur garnettii	ENSOGAG00000024374	1 retrocopy	retro_ogar_914,
Ochotona princeps	ENSOPRG00000014606	1 retrocopy	retro_opri_1137,
Pongo abelii	ENSPPYG00000005306	1 retrocopy	retro_pabe_3785,
Sorex araneus	ENSSARG00000004428	1 retrocopy	retro_sara_594,
Sarcophilus harrisii	ENSSHAG00000007140	1 retrocopy	retro_shar_591,
Tarsius syrichta	ENSTSYG00000002170	1 retrocopy	retro_tsyr_238,
Tursiops truncatus	ENSTTRG00000012556	1 retrocopy	retro_ttru_1285,