RetrogeneDB ID: retro_ocun_1141

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:9894203..9894600(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS10
• Ensembl ID: ENSOCUG00000016697
• Aliases: None
• Description: mitochondrial ribosomal protein S10 [Source:HGNC Symbol;Acc:14502]

Sequence

>retro_ocun_1141
GTAACCACCTCTGATGACAAGACACATTGCATAAACAGCTGTCCATTTTAGTAAAACGCCACGAGAAAACTGCATTGGAC
ATTATGGACACTTTGCTGTGCTTGTTGCAAAAGGACTTGGTATCTTTACTGAAGTACATGAACCTCCAAGGAAAACAGAG
CAATTTACTGTTTTCAAATCAGCGTGCATTTCCCAGGAGCACAGGGCTGGGTGTGAAATGCGGACACTTCACAGGTGTTT
CCTGTGAGAACACTAACTGGAGTACAGCAGGTGTCCTCTCGGAAAACATTCAGTGAAGCCTGCTGAAGGGGTTGCCATGG
AAGTCATAAAGACTCAGGCAGAGCTGGTACCAGAACACAGCGAGGAGCCAACGTGGGAAATGATACCAAGTCCCCGG

Alignment

ORF - retro_ocun_1141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.12 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ITVSDEP-DTLYKRLSILVKGHDKAVLD-SYEYFAVLAAKELGITIKVHEPPRKIERFTLLKSVHIFKKH
          .T.SD...DTL.K.LSILVK.H.K..LD..Y..FAVL.AK.LGI...VHEPPRK.E.FT..KS..I...H
Retrocopy VTTSDDK<DTLHKQLSILVKRHEKTALD<HYGHFAVLVAKGLGIFTEVHEPPRKTEQFTVFKSACISQEH

Parental  RVQYEMRTLYRC-LELERLTG-STADVYLEYIQRNL-PEGVAMEVTKTHLERLPEHIKEPIWETVPEEK
          R...EMRTL.RC......LTG.STA.V..E.IQ..L..EGVAMEV.KT..E..PEH..EP.WE..P...
Retrocopy RAGCEMRTLHRC<FPVRTLTG<STAGVLSENIQ*SL<AEGVAMEVIKTQAELVPEHSEEPTWEMIPSPR

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	45.09 RPM
SRP017611_kidney	0.00 RPM	24.63 RPM
SRP017611_liver	0.00 RPM	13.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1141 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1141 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002081	1 retrocopy	retro_dord_412,
Homo sapiens	ENSG00000048544	1 retrocopy	retro_hsap_4157,
Gorilla gorilla	ENSGGOG00000012808	1 retrocopy	retro_ggor_2532,
Microcebus murinus	ENSMICG00000011379	1 retrocopy	retro_mmur_321,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Oryctolagus cuniculus	ENSOCUG00000016697	1 retrocopy	retro_ocun_1141 ,
Pongo abelii	ENSPPYG00000016613	1 retrocopy	retro_pabe_3456,
Pan troglodytes	ENSPTRG00000018169	1 retrocopy	retro_ptro_2826,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Ictidomys tridecemlineatus	ENSSTOG00000027016	1 retrocopy	retro_itri_1183,