RetrogeneDB ID: retro_mmus_259

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:5120652..5121135(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000068706
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Atp5h
• Ensembl ID: ENSMUSG00000034566
• Aliases: Atp5h, 0610009D10Rik
• Description: ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d [Source:MGI Symbol;Acc:MGI:1918929]

Sequence

>retro_mmus_259
ATGGCTGGGCGTAAACTTGCTCTAAAAACCATTGATTGGGTATCTTTTGTGGAGGTCATGCCCCAAAATCAGAAGGCAAT
TGGAAATGCCCTGAAGTCCTGGAATGAGACCTTCCACGCCAGGTTGGCTAGTCTGTCTGAGAAACCACCTGCGATTGACT
GGGCTTACTACAGGGCCAATGTGGCCAAGCCTGGCTTGGTGGATGATTTTGAAAAGAAGTATAATGCCCTGAAGATTCCT
GTGCCTGAGGATAAATACACAGCCCTGGTGGACCAGGAGGAGAAGGAGGATGTGAAGAGCTGTGCTGAATTTGTGTCTGG
ATCCCAGCTCAGGATCCAGGAGTATGAGAAGCAGCTGGAGAAAATGAGGAACATAATTCCCTTTGACCAGATGACCATTG
ATGACTTGAATGAGATCTTCCCAGAAACCAAGCTGGACAAGAAGTACCCGTACTGGCCCCACCAGCCCATCGAGAACCTG
TGA

Alignment

ORF - retro_mmus_259 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGRKLALKTIDWVSFVEVMPQNQKAIGNALKSWNETFHARLASLSEKPPAIDWAYYRANVAKPGLVDDF
          MAGRKLALKTIDWVSFVEVMPQNQKAIGNALKSWNETFHARLASLSEKPPAIDWAYYRANVAKPGLVDDF
Retrocopy MAGRKLALKTIDWVSFVEVMPQNQKAIGNALKSWNETFHARLASLSEKPPAIDWAYYRANVAKPGLVDDF

Parental  EKKYNALKIPVPEDKYTALVDQEEKEDVKSCAEFVSGSQLRIQEYEKQLEKMRNIIPFDQMTIDDLNEIF
          EKKYNALKIPVPEDKYTALVDQEEKEDVKSCAEFVSGSQLRIQEYEKQLEKMRNIIPFDQMTIDDLNEIF
Retrocopy EKKYNALKIPVPEDKYTALVDQEEKEDVKSCAEFVSGSQLRIQEYEKQLEKMRNIIPFDQMTIDDLNEIF

Parental  PETKLDKKKYPYWPHQPIENL
          PETKLDKK.YPYWPHQPIENL
Retrocopy PETKLDKK-YPYWPHQPIENL

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	0.47 RPM	86.98 RPM
SRP007412_cerebellum	0.30 RPM	92.53 RPM
SRP007412_heart	3.70 RPM	368.68 RPM
SRP007412_kidney	1.48 RPM	241.89 RPM
SRP007412_liver	0.30 RPM	91.29 RPM
SRP007412_testis	0.37 RPM	58.45 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_259 in 4 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	15:5121126..5121857
ENCFF001XVA	POLR2A	15:5121904..5122256
ENCFF001YIJ	POLR2A	15:5115190..5123695
ENCFF001YJZ	POLR2A	15:5121070..5122908
ENCFF001YKA	POLR2A	15:5115258..5125624

EST

No EST(s) were mapped for retro_mmus_259 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_40346	127 libraries	371 libraries	547 libraries	24 libraries	3 libraries

The graphical summary, for retro_mmus_259 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_259 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 113 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009115	6 retrocopies	retro_amel_1265, retro_amel_1560, retro_amel_1615, retro_amel_1672, retro_amel_1823, retro_amel_921,
Bos taurus	ENSBTAG00000021227	5 retrocopies	retro_btau_1663, retro_btau_319, retro_btau_608, retro_btau_674, retro_btau_823,
Canis familiaris	ENSCAFG00000004703	1 retrocopy	retro_cfam_178,
Callithrix jacchus	ENSCJAG00000014622	15 retrocopies	retro_cjac_1005, retro_cjac_1036, retro_cjac_1159, retro_cjac_1740, retro_cjac_1825, retro_cjac_1831, retro_cjac_2096, retro_cjac_2196, retro_cjac_2488, retro_cjac_2543, retro_cjac_2849, retro_cjac_3141, retro_cjac_456, retro_cjac_737, retro_cjac_739,
Cavia porcellus	ENSCPOG00000004022	3 retrocopies	retro_cpor_1429, retro_cpor_547, retro_cpor_972,
Dasypus novemcinctus	ENSDNOG00000006913	2 retrocopies	retro_dnov_1725, retro_dnov_412,
Equus caballus	ENSECAG00000009487	2 retrocopies	retro_ecab_526, retro_ecab_706,
Echinops telfairi	ENSETEG00000003217	8 retrocopies	retro_etel_133, retro_etel_172, retro_etel_1894, retro_etel_266, retro_etel_283, retro_etel_419, retro_etel_713, retro_etel_97,
Felis catus	ENSFCAG00000022888	2 retrocopies	retro_fcat_636, retro_fcat_837,
Homo sapiens	ENSG00000167863	4 retrocopies	retro_hsap_1133, retro_hsap_1561, retro_hsap_4134, retro_hsap_4223,
Gorilla gorilla	ENSGGOG00000013716	4 retrocopies	retro_ggor_1186, retro_ggor_2778, retro_ggor_2827, retro_ggor_884,
Macropus eugenii	ENSMEUG00000009346	1 retrocopy	retro_meug_788,
Microcebus murinus	ENSMICG00000017484	4 retrocopies	retro_mmur_1216, retro_mmur_593, retro_mmur_785, retro_mmur_895,
Myotis lucifugus	ENSMLUG00000010620	7 retrocopies	retro_mluc_1267, retro_mluc_1386, retro_mluc_1722, retro_mluc_2076, retro_mluc_2421, retro_mluc_464, retro_mluc_833,
Macaca mulatta	ENSMMUG00000011647	1 retrocopy	retro_mmul_208,
Mustela putorius furo	ENSMPUG00000014048	9 retrocopies	retro_mputfur_1266, retro_mputfur_1466, retro_mputfur_151, retro_mputfur_1589, retro_mputfur_1617, retro_mputfur_268, retro_mputfur_301, retro_mputfur_405, retro_mputfur_904,
Mus musculus	ENSMUSG00000034566	6 retrocopies	retro_mmus_1296, retro_mmus_168, retro_mmus_1793, retro_mmus_259 , retro_mmus_2794, retro_mmus_298,
Nomascus leucogenys	ENSNLEG00000000561	4 retrocopies	retro_nleu_1057, retro_nleu_1728, retro_nleu_2478, retro_nleu_927,
Oryctolagus cuniculus	ENSOCUG00000015537	2 retrocopies	retro_ocun_1332, retro_ocun_655,
Otolemur garnettii	ENSOGAG00000001990	4 retrocopies	retro_ogar_1372, retro_ogar_2438, retro_ogar_436, retro_ogar_736,
Procavia capensis	ENSPCAG00000015330	2 retrocopies	retro_pcap_160, retro_pcap_296,
Pongo abelii	ENSPPYG00000008615	4 retrocopies	retro_pabe_1291, retro_pabe_3415, retro_pabe_3416, retro_pabe_3470,
Pan troglodytes	ENSPTRG00000009628	4 retrocopies	retro_ptro_1050, retro_ptro_2810, retro_ptro_2867, retro_ptro_769,
Rattus norvegicus	ENSRNOG00000003626	1 retrocopy	retro_rnor_197,
Sorex araneus	ENSSARG00000013370	3 retrocopies	retro_sara_434, retro_sara_473, retro_sara_474,
Sarcophilus harrisii	ENSSHAG00000018708	2 retrocopies	retro_shar_711, retro_shar_726,
Ictidomys tridecemlineatus	ENSSTOG00000015154	2 retrocopies	retro_itri_1086, retro_itri_846,
Tupaia belangeri	ENSTBEG00000012545	3 retrocopies	retro_tbel_1122, retro_tbel_1184, retro_tbel_728,
Tursiops truncatus	ENSTTRG00000002618	2 retrocopies	retro_ttru_1298, retro_ttru_739,