RetrogeneDB ID: retro_rnor_2679

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:44850638..44851143(+)
• Located in intron of: ENSRNOG00000018830

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nme4
• Ensembl ID: ENSRNOG00000049152
• Aliases: None
• Description: nucleoside diphosphate kinase, mitochondrial [Source:RefSeq peptide;Acc:NP_001102948]

Sequence

>retro_rnor_2679
TTGTGTGGCCATCCTCTTGATGCCTGCTGGTGCGCCCTGGTACTGCAGGGCCTCCCTGGCCCCAGGAGCAGACCCTGATT
GCTGTGAAGCCACAGGGGGTACAGCAGAGGCTGATGTAAACTCCGATGCAATGCTCTGAGAGGTGGGGCTTCAAGCTGGT
AGGGATGAAGATGTTTTCGGGCACCAGAGAGCATCCTTGCTGAGCACGGCCGAGACCTCCAGCAGAAGCCATCCTACCCA
GCGCTTATCAGCAACATGAGCCCTGGGGTCTGTGGTGGCCATAGTCTGGGAAGTGTACAATGTGTCCACATCTCAAGGAC
AGTGATAGGACACACTGGCTCAACGGAGAAAGCCCCCGGGGACAATCAGGGGTGACTTCAGTGTTTATATCAGCAGAAAG
GTAGCAAGTCCTAAGGACAGGGCCCATACGGAGATCCAGCTATGGTTTCAGGGCAGCGAACCCTTGAACTGAGCAAACGG
TGGTCACCACAGCAGCTGCTACCCA

Alignment

ORF - retro_rnor_2679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 92.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LCG-PRFQCLLVRPSSGGPPWPQERTLVAVKPDGVQRRLVGTVIHRFERRGFKLVGMKM-LQAPESILAE
          LCG.P...CLLVRP...GPPWPQE.TL.AVKP.GVQ.RL..T.....ER.GFKLVGMKM...APESILAE
Retrocopy LCG<PSS*CLLVRPGTAGPPWPQEQTLIAVKPQGVQQRLM*TPMQCSERWGFKLVGMKM>FRAPESILAE

Parental  HYRDLQRKPFYPALISYMSS-GPVVAMVWEGHNV-VHISRAMIGHTDSTEAA-PGTIRGDFSVHISRNVI
          H.RDLQ.KP.YPALIS.MS..G.VVA.VWE..NV.VHISR..IGHT.STE.A.PGTIRGDFSV.ISR.V.
Retrocopy HGRDLQQKPSYPALISNMSP>GSVVAIVWEVYNV<VHISRTVIGHTGSTEKA>PGTIRGDFSVYISRKVA

Parental  HASDSVDGAQREIELWFQSSELLNWADGGHHSSCYP
          ...D....A..EI.LWFQ.SE.LN.A.GGHHSSCYP
Retrocopy SPKDR---AHTEIQLWFQGSEPLN*ANGGHHSSCYP

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	0.93 RPM
SRP017611_kidney	0.00 RPM	12.35 RPM
SRP017611_liver	0.00 RPM	0.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2679 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2679 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_309

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007077	3 retrocopies	retro_amel_1271, retro_amel_216, retro_amel_238,
Canis familiaris	ENSCAFG00000019677	4 retrocopies	retro_cfam_1267, retro_cfam_2209, retro_cfam_447, retro_cfam_71,
Cavia porcellus	ENSCPOG00000006496	1 retrocopy	retro_cpor_1076,
Echinops telfairi	ENSETEG00000014875	1 retrocopy	retro_etel_1833,
Felis catus	ENSFCAG00000008300	3 retrocopies	retro_fcat_1013, retro_fcat_1512, retro_fcat_1672,
Homo sapiens	ENSG00000103202	1 retrocopy	retro_hsap_1740,
Gorilla gorilla	ENSGGOG00000004512	1 retrocopy	retro_ggor_2259,
Macropus eugenii	ENSMEUG00000005455	5 retrocopies	retro_meug_1027, retro_meug_1427, retro_meug_1981, retro_meug_1999, retro_meug_694,
Myotis lucifugus	ENSMLUG00000010061	1 retrocopy	retro_mluc_388,
Macaca mulatta	ENSMMUG00000000612	1 retrocopy	retro_mmul_1221,
Mustela putorius furo	ENSMPUG00000016017	3 retrocopies	retro_mputfur_1024, retro_mputfur_1067, retro_mputfur_846,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Nomascus leucogenys	ENSNLEG00000008068	1 retrocopy	retro_nleu_2719,
Otolemur garnettii	ENSOGAG00000025808	1 retrocopy	retro_ogar_2689,
Pongo abelii	ENSPPYG00000006908	1 retrocopy	retro_pabe_1442,
Pan troglodytes	ENSPTRG00000007541	1 retrocopy	retro_ptro_1220,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679 ,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Ictidomys tridecemlineatus	ENSSTOG00000004798	1 retrocopy	retro_itri_1629,
Tursiops truncatus	ENSTTRG00000009157	2 retrocopies	retro_ttru_393, retro_ttru_688,
Vicugna pacos	ENSVPAG00000010316	1 retrocopy	retro_vpac_150,