RetrogeneDB ID: retro_ocun_1728

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018826:205890..206156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME1
• Ensembl ID: ENSOCUG00000022135
• Aliases: None
• Description: NME/NM23 nucleoside diphosphate kinase 1 (NME1), mRNA [Source:RefSeq mRNA;Acc:NM_001204749]

Sequence

>retro_ocun_1728
ACTATAACCAACACAGAGAATACCTTCATCACCATCCAGCCCCATGAGGGCCGGGGGGTGCTTGTGGAAGAGACCACCAA
ATGTCTGGAGCAGAAGGGATTCTGCCTTGTCAGTCTGAAATTAATGCAGGCGTCCGACACCTCCTCCAGGGTCACTACAG
TGACGTGAAGGACCAGCAGTTATTTGCCCACCCGGTGAAATGCATGCACTCAGGGCCCTGGGTCGCCATGGTGTGGGAGG
AACTGAATGTGGTGAAGACGGGCCGA

Alignment

ORF - retro_ocun_1728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 58.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TMANTERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVSLKLMQASED-LLREHYIDLKDRPFFPGLVKYM
          T..NTE.TFI.I.P......LV.E..K..EQKGF.LVSLKLMQAS...LL..HY.D.KD...F...VK.M
Retrocopy TITNTENTFITIQPHEGRGVLVEETTKCLEQKGFCLVSLKLMQASDT<LLQGHYSDVKDQQLFAHPVKCM

Parental  HSGPVVAMVWEGLNVVKTGR
          HSGP.VAMVWE.LNVVKTGR
Retrocopy HSGPWVAMVWEELNVVKTGR

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	56.40 RPM
SRP017611_kidney	0.00 RPM	18.24 RPM
SRP017611_liver	0.00 RPM	6.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1728 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1728 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029, retro_nleu_1030,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728 ,
Oryctolagus cuniculus	ENSOCUG00000024946	1 retrocopy	retro_ocun_418,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,