RetrogeneDB ID: retro_rnor_1106

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:45397000..45397412(+)
• Located in intron of: ENSRNOG00000014603

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G3
• Ensembl ID: ENSRNOG00000001596
• Aliases: None
• Description: ATP synthase lipid-binding protein, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_446208]

Sequence

>retro_rnor_1106
GTGTTTGCCTGTGCCAAGCTTGCCCACACCCCTACTCTGATCCAAGCCAGACCTAGAGTTGCATATAGACCAATTTCTGC
ATCAGTGTTATCTCAACCAGAGACTAGGACTGGAGAGGGCTCTACAGTATTTAATGGGGACCAGAATGCTCTGTGTCAGC
TGACTGGAAGGGAGTTCCAGACCAGTGTAATCAACAGAGATGATACTGATGCCAAACTCATTGGTGTGGGCACTGCCACA
GTAGGAGTTGCTGGTTCTAGTGCTGGTATTGGGAGTCTTTGGCAGTCTTATCATTGGTTTTGCCAGAGACCCTTGACTGA
AGCAGCAGCTGTTCTCAGACGCTCTCCTGGGATTTGCCTTGTCTGAAGCTATGGGTATCTTTTGTTTGATGGTTGCATTC
TTGATCTTGTTT

Alignment

ORF - retro_rnor_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 98.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFACAKLARTPALIRAGSRVAYRPISASVLSRPETRTGEGSTVFNGAQNGVCQLIRREFQTSVISRDIDT
          .FACAKLA.TP.LI.A..RVAYRPISASVLS.PETRTGEGSTVFNG.QN..CQL..REFQTSVI.RD.DT
Retrocopy VFACAKLAHTPTLIQARPRVAYRPISASVLSQPETRTGEGSTVFNGDQNALCQLTGREFQTSVINRD-DT

Parental  AAKFIGAGAATVGVAGSGAG-IGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILF
          .AK.IG.G.ATVGVAGS.AG..G.VFGSLIIG.AR.P.LKQQLFS.A.LGFALSEAMG.FCLMVAFLILF
Retrocopy DAKLIGVGTATVGVAGSSAG>LG-VFGSLIIGFARDP*LKQQLFSDALLGFALSEAMGIFCLMVAFLILF

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	124.45 RPM
SRP017611_kidney	0.00 RPM	408.44 RPM
SRP017611_liver	0.00 RPM	156.39 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1106 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1106 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106 ,
Rattus norvegicus	ENSRNOG00000007235	5 retrocopies	retro_rnor_1342, retro_rnor_2240, retro_rnor_529, retro_rnor_64, retro_rnor_880,
Rattus norvegicus	ENSRNOG00000015320	6 retrocopies	retro_rnor_1286, retro_rnor_1490, retro_rnor_1939, retro_rnor_2699, retro_rnor_2738, retro_rnor_2910,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324, retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,