RetrogeneDB ID: retro_rnor_1183

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:25070133..25070610(+)
• Located in intron of: ENSRNOG00000026310

Retrocopy information

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

Parental gene information

• Parental gene symbol: Bnip3l
• Ensembl ID: ENSRNOG00000009820
• Aliases: Bnip3l, Nix
• Description: BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like [Source:RefSeq peptide;Acc:NP_543164]

Sequence

>retro_rnor_1183
ATGTCTAACTTAGTTGAGCAGTCGCTGCCCCTGCATAACAACTGTGAGGAAGGGGAGCTATCCTCTGCCACCACCCGCTG
GCCTCAACGGTTCCTTGGTGGAGTTACTAATGAACAGCAGCAAGGGCAATGATAGTGGAAATGGGAAGAATTGGGGGCTG
GAGCATGTTCCTTCCTGGCCTTCCAGTCACAGTGGAGACATGGAGTAGATACTTCTGGGTGCATAGCATGAGTCGTAACA
GAGCAGCTTAAGAGGCAGTTCTCACAGTGATTGCTCTTCACCACAAGAAGATGGGCAGGTCATGTTTAATGTTGAGATGC
TTACCAGTAAGGACCACAACTCTCAGTTAGAAGAAGAAGTTGTAGAAGGAGAAAAAGAAGTTGAGACTTTGAAGAAAAGT
GCAGACTGGGTATCAGACTGGTCCAGTAGACCCAAAACATCCCACCCAAAAAGTTCCATTTCAGACACCCTAAACGT

Alignment

ORF - retro_rnor_1183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.61 %
• Parental protein coverage: 74.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSHLVEPPPPLHNNNNNCEEGEQS-LPPPAGLNSSWVELPMNSSNGNGNGNGKNGGLEHVPSSSSIHNGD
          MS.LVE...PLH...NNCEEGE.S.LPPPAGLN.S.VEL.MNSS.GN..GNGKN.GLEHVPS..S.H.GD
Retrocopy MSNLVEQSLPLH---NNCEEGELS>LPPPAGLNGSLVELLMNSSKGNDSGNGKNWGLEHVPSWPSSHSGD

Parental  MEKILLDAQHESGQSSSRGSSHCDSPSPQEDGQIMFDVEMHTSRDHSSQSEEEVVDGEKEVEALKKSADW
          ME.ILL.A.HES.QSS.RGSSH.D..SPQEDGQ.MF.VEM.TS.DH.SQ.EEEVV.GEKEVE.LKKSADW
Retrocopy ME*ILLGA*HES*QSSLRGSSHSDCSSPQEDGQVMFNVEMLTSKDHNSQLEEEVVEGEKEVETLKKSADW

Parental  VSDWSSRP-ENIPPKEFLFRHPKR
          VSDWSSRP..NIPPK.F.FRHPKR
Retrocopy VSDWSSRP<QNIPPKKFHFRHPKR

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	122.73 RPM
SRP017611_kidney	0.00 RPM	129.17 RPM
SRP017611_liver	0.00 RPM	59.03 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1183 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1183 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021307	4 retrocopies	retro_btau_1148, retro_btau_1170, retro_btau_1790, retro_btau_449,
Choloepus hoffmanni	ENSCHOG00000007732	3 retrocopies	retro_chof_2356, retro_chof_2475, retro_chof_980,
Dasypus novemcinctus	ENSDNOG00000016179	1 retrocopy	retro_dnov_2101,
Dipodomys ordii	ENSDORG00000009336	1 retrocopy	retro_dord_169,
Erinaceus europaeus	ENSEEUG00000006302	1 retrocopy	retro_eeur_269,
Echinops telfairi	ENSETEG00000012037	3 retrocopies	retro_etel_1178, retro_etel_1428, retro_etel_603,
Felis catus	ENSFCAG00000030159	2 retrocopies	retro_fcat_616, retro_fcat_944,
Macropus eugenii	ENSMEUG00000011173	1 retrocopy	retro_meug_962,
Myotis lucifugus	ENSMLUG00000014949	1 retrocopy	retro_mluc_2192,
Mustela putorius furo	ENSMPUG00000000829	1 retrocopy	retro_mputfur_297,
Mus musculus	ENSMUSG00000022051	2 retrocopies	retro_mmus_482, retro_mmus_849,
Oryctolagus cuniculus	ENSOCUG00000010542	1 retrocopy	retro_ocun_1460,
Otolemur garnettii	ENSOGAG00000003163	2 retrocopies	retro_ogar_1039, retro_ogar_2651,
Ochotona princeps	ENSOPRG00000016284	1 retrocopy	retro_opri_1105,
Rattus norvegicus	ENSRNOG00000009820	1 retrocopy	retro_rnor_1183 ,
Rattus norvegicus	ENSRNOG00000017243	3 retrocopies	retro_rnor_1070, retro_rnor_2645, retro_rnor_2732,
Sus scrofa	ENSSSCG00000009658	1 retrocopy	retro_sscr_511,
Ictidomys tridecemlineatus	ENSSTOG00000004029	1 retrocopy	retro_itri_1525,
Tupaia belangeri	ENSTBEG00000006361	2 retrocopies	retro_tbel_3371, retro_tbel_4006,
Tarsius syrichta	ENSTSYG00000011036	4 retrocopies	retro_tsyr_1182, retro_tsyr_1602, retro_tsyr_162, retro_tsyr_1997,
Tursiops truncatus	ENSTTRG00000004862	1 retrocopy	retro_ttru_725,
Vicugna pacos	ENSVPAG00000000509	2 retrocopies	retro_vpac_349, retro_vpac_534,