RetrogeneDB ID: retro_ocun_1936

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:72644756..72645062(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL27
• Ensembl ID: ENSOCUG00000004601
• Aliases: None
• Description: mitochondrial ribosomal protein L27 [Source:HGNC Symbol;Acc:14483]

Sequence

>retro_ocun_1936
TCAGTCAGATATACATACAAGAAGACAGGCAGCAGCTTTAAAAACCTCAGTGAAAAGTGACCAGGCAAGAGCTTTGGCAT
CAAGAAAATGGAAGGTCACTATGTGCATTCTGGAGACATCCTTGGGACTCGGCGCCAGTTCCGCTGGCACCCAGGTGCCC
ACATGGGGCTGGGGAAGAAGTGCCTGTACACGTTGCAGGAGGGGATAGTCTGCTACACCAAGGAGGTCTATATGCCCAGT
CCTAGCAACTCAGAGGCCATGGATCTGGTCACCAGGCTGCCCAGAGGAGCTGTGCTCTGAAAGACA

Alignment

ORF - retro_ocun_1936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.64 %
• Parental protein coverage: 69.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVRYASKKTGGSSKNLGGKAPGKRFGIKKLEGHYVHAGNILGTQRQFRWHPGAHVGLGNKKCLYALEEGI
          .VRY..KKTG.S.KNL..K.PGK.FGIKK.EGHYVH.G.ILGT.RQFRWHPGAH.GLG.KKCLY.L.EGI
Retrocopy SVRYTYKKTGSSFKNLSEK*PGKSFGIKKMEGHYVHSGDILGTRRQFRWHPGAHMGLG-KKCLYTLQEGI

Parental  VRYTKEVYVPNPSNSEAVDLVTRLPRGAVLYKT
          V.YTKEVY.P.PSNSEA.DLVTRLPRGAVL.KT
Retrocopy VCYTKEVYMPSPSNSEAMDLVTRLPRGAVL*KT

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	17.22 RPM
SRP017611_kidney	0.00 RPM	39.63 RPM
SRP017611_liver	0.00 RPM	7.17 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1936 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1936 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017031	1 retrocopy	retro_cfam_1454,
Choloepus hoffmanni	ENSCHOG00000005103	1 retrocopy	retro_chof_943,
Callithrix jacchus	ENSCJAG00000018851	2 retrocopies	retro_cjac_28, retro_cjac_378,
Dasypus novemcinctus	ENSDNOG00000023845	2 retrocopies	retro_dnov_1233, retro_dnov_1731,
Erinaceus europaeus	ENSEEUG00000010549	3 retrocopies	retro_eeur_126, retro_eeur_22, retro_eeur_9,
Echinops telfairi	ENSETEG00000014252	2 retrocopies	retro_etel_13, retro_etel_893,
Microcebus murinus	ENSMICG00000009698	1 retrocopy	retro_mmur_624,
Macaca mulatta	ENSMMUG00000017231	1 retrocopy	retro_mmul_64,
Mus musculus	ENSMUSG00000024414	2 retrocopies	retro_mmus_1696, retro_mmus_2918,
Oryctolagus cuniculus	ENSOCUG00000004601	2 retrocopies	retro_ocun_1026, retro_ocun_1936 ,
Otolemur garnettii	ENSOGAG00000005385	1 retrocopy	retro_ogar_53,