RetrogeneDB ID: retro_mmus_482

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:128005787..128006438(-)
• Located in intron of: ENSMUSG00000036086

Retrocopy information

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

Parental gene information

• Parental gene symbol: Bnip3l
• Ensembl ID: ENSMUSG00000022051
• Aliases: Bnip3l, C86132, D14Ertd719e, Nip3L, Nix
• Description: BCL2/adenovirus E1B interacting protein 3-like [Source:MGI Symbol;Acc:MGI:1332659]

Sequence

>retro_mmus_482
ATGTCTCACTTAGTGGAGCCACCGCTGCTGCCCTTGCACAACAACAACTTCGAGGAAGGGGAGCAGCCCCTGCAGCCGCC
CCGCTGGCCTCAACAGTTCCTGGGTGGAGCTACCCATGAACAGCAGCAAAGGCAATGAGAATGGAAATGGGAAGAATGGG
GGGCTGGAGCACGTTCCTTCCTCGTCTTCCATCCACAATGGAGACATGGAGAAGATCCTCCTGGATGCACAGCATGAGTC
GGGACAGAGCAGCTCAAGAGGCAGTTGGCACTGTGACAGCCCTTCACCACAAGAAGATGGGCAGATCATGTTTGATGTTG
AGATGCATACCAGCAGGGACCACAGCTCTCAGTCAGAAGAAGAAGTTGTAGAAGGAGAAAAGGAAGTTGAGGCTTTGAAG
AAAAGTGCAGACTGGGTATCAGACTGGTCCAGTAGACCCGAAAACATCCCCCCCAAAGAGTTCCATTTCAGACACCCTAA
ACGTGCTGCGTCTCTAAGCATGAGGAAGAGTGGAGCCATGAAGAAAGGGGGCATTTTCTCTGCAGAGTTCCTAAAAGTCT
TCATCCCATCTCTCTTCCTTTCTCATGTGCTGGCCTGGGGCTGGGCATCTATATTGGAAAATGACTGAGCACACCTTCTG
CCAGCACCTAC

Alignment

ORF - retro_mmus_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSHLVEPPP-PLHNNNNNCEEGEQPLPPP-AGLNSSWVELPMNSSNGNENGNGKNGGLEHVPSSSSIHNG
          MSHLVEPP..PLHNNN...EEGEQPL.PP.AGLNSSWVELPMNSS.GNENGNGKNGGLEHVPSSSSIHNG
Retrocopy MSHLVEPPLLPLHNNN--FEEGEQPLQPP>AGLNSSWVELPMNSSKGNENGNGKNGGLEHVPSSSSIHNG

Parental  DMEKILLDAQHESGQSSSRGSSHCDSPSPQEDGQIMFDVEMHTSRDHSSQSEEEVVEGEKEVEALKKSAD
          DMEKILLDAQHESGQSSSRGS.HCDSPSPQEDGQIMFDVEMHTSRDHSSQSEEEVVEGEKEVEALKKSAD
Retrocopy DMEKILLDAQHESGQSSSRGSWHCDSPSPQEDGQIMFDVEMHTSRDHSSQSEEEVVEGEKEVEALKKSAD

Parental  WVSDWSSRPENIPPKEFHFRHPKRAASLSMRKSGAMKKGGIFSAEFLKVFIPSLFLSHVLA-LGLGIYIG
          WVSDWSSRPENIPPKEFHFRHPKRAASLSMRKSGAMKKGGIFSAEFLKVFIPSLFLSHVLA.LGLGIYIG
Retrocopy WVSDWSSRPENIPPKEFHFRHPKRAASLSMRKSGAMKKGGIFSAEFLKVFIPSLFLSHVLA<LGLGIYIG

Parental  KRLSTPSASTY
          K.LSTPSASTY
Retrocopy K*LSTPSASTY

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
SRP007412_brain	0.00 RPM	74.29 RPM
SRP007412_cerebellum	0.00 RPM	42.81 RPM
SRP007412_heart	0.06 RPM	29.60 RPM
SRP007412_kidney	0.02 RPM	43.08 RPM
SRP007412_liver	0.05 RPM	41.18 RPM
SRP007412_testis	0.00 RPM	19.21 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_482 was not detected

EST

No EST(s) were mapped for retro_mmus_482 retrocopy.

TSS

No TSS is located nearby retro_mmus_482 retrocopy 5' end.

Lab

retro_mmus_482 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_482 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 40 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,
Mus musculus	ENSMUSG00000078566	4 retrocopies	retro_mmus_1194, retro_mmus_1195, retro_mmus_2207, retro_mmus_3577,
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,
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,