RetrogeneDB ID: retro_ocun_850

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:94138019..94138513(-)
• Located in intron of: ENSOCUG00000013272

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000022455
• Aliases: None
• Description: None

Sequence

>retro_ocun_850
ATGACTGAGTAAAGACTGGTGGTGGTTGGAGCAAGTGGTGCTGGGAGAGTGCACTGATAATCCAGCTGATCCAGAACCAC
TTTGTGGATAAATATGATTCCCCCATAGAGGATTCTTACTGAAAATAGGTGATTATAGATGGCAAAGCCTGTCTGTTGGA
CATTCTGGATACAGCTGGACAAGAGGAGTACAGTGCCATGAGAGACCAATACATGAGGACAGGCAAAGGCTTCCTCTATG
TATTTGCCATCAATAATAGCAAATCATTTAGAGATATTAACCTCTATACAGAGCAGATTAAGCATGTGAAAGACTCAGAT
GGTGTACCTATGGTGCTGGTAGGAAACAAGTGTGATTTACCAACAAGGACAATTGACATGAAACAAGCTGATGAACTGGC
TAAGAGTTAAGGGATTCTGTTTATTGAAACCTCAGCCAAGACCAGACAGGGTATTGAAGATGCCTTTTTCACTCTGGTAA
GAGAAATATGACAA

Alignment

ORF - retro_ocun_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.53 %
• Parental protein coverage: 87.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGVGK-SALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRD
          MTE..LVVVGA.G.G..SAL.IQLIQNHFVD.YD..IEDSY.K.V.IDG..CLLDILDTAGQEEYSAMRD
Retrocopy MTE*RLVVVGASGAGR<SALIIQLIQNHFVDKYDSPIEDSY*K*VIIDGKACLLDILDTAGQEEYSAMRD

Parental  QYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGI
          QYMRTG.GFL.VFAINNSKSF.DINLY.EQIK.VKDSD.VPMVLVGNKCDLPTRT.D.KQA.ELAKS.GI
Retrocopy QYMRTGKGFLYVFAINNSKSFRDINLYTEQIKHVKDSDGVPMVLVGNKCDLPTRTIDMKQADELAKS*GI

Parental  PFIETSAKTRQGVEDAFYTLVREIRQ
          .FIETSAKTRQG.EDAF.TLVREI.Q
Retrocopy LFIETSAKTRQGIEDAFFTLVREI*Q

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	9.66 RPM
SRP017611_kidney	0.00 RPM	24.73 RPM
SRP017611_liver	0.00 RPM	8.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_850 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_850 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017134	1 retrocopy	retro_amel_885,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400,
Felis catus	ENSFCAG00000019026	1 retrocopy	retro_fcat_1191,
Loxodonta africana	ENSLAFG00000020706	1 retrocopy	retro_lafr_492,
Macropus eugenii	ENSMEUG00000002675	1 retrocopy	retro_meug_2136,
Myotis lucifugus	ENSMLUG00000022354	1 retrocopy	retro_mluc_741,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51,
Oryctolagus cuniculus	ENSOCUG00000022455	1 retrocopy	retro_ocun_850 ,
Oryctolagus cuniculus	ENSOCUG00000029552	5 retrocopies	retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619,
Sus scrofa	ENSSSCG00000006753	1 retrocopy	retro_sscr_520,