RetrogeneDB ID: retro_mmus_3045

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:81222364..81222874(-)
• Located in intron of: ENSMUSG00000025584

Retrocopy information

• Ensembl ID: ENSMUSG00000083774
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Timm17a
• Ensembl ID: ENSMUSG00000062580
• Aliases: Timm17a, 17kDa, mTim17a
• Description: translocase of inner mitochondrial membrane 17a [Source:MGI Symbol;Acc:MGI:1343131]

Sequence

>retro_mmus_3045
ATGGAGGAATACGTGAGAGAGCCGTGCCCCTGGCAAATTGTGGATGACTGTGGCAGTACGTTTATGGGCACCATAGGTGG
CGGCATCTTCCAGGCCTTCAAAGGTTTTCGAAATTCTCCAGTGGGAATAAACCACAGACTCCGAGGGAGTTTGACAGCTA
TTAAAACCAGGACTCCACAGTTGGGAGGTAGCTTTGCAGTTTGGGGAGGATTGTTTTCCACGATTGACTGCAGTATGGTT
CAAATACGAGGCAAAGAAGACCCCTGGAACTCCATCACTAGCGGTGCCTTAACAGGAGCCATCCTGGCAGCAAGAAATGG
ACCGGTAGCCATGGTTGGGTCCGCTGCAATGGGCGCCATTCTCCTAGCTTTAATTGAAGGAGCTGGTATCTTGCTGACAA
GATTTGCCTCTGCACAGTTTCCCAATGGCCCTCAATTCGCTGAAGATCACTCCCAGTTGCCTTCCAGCCAGTTGCCATCC
TCACTGTTTGGAGACCACCGACAGTATCAG

Alignment

ORF - retro_mmus_3045 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEYAREPCPWRIVDDCGGAFTMGTIGGGIFQAFKGFRNSPVGINHRLRGSLTAIKTRAPQLGGSFAVWG
          MEEY.REPCPW.IVDDCG..F.MGTIGGGIFQAFKGFRNSPVGINHRLRGSLTAIKTR.PQLGGSFAVWG
Retrocopy MEEYVREPCPWQIVDDCGSTF-MGTIGGGIFQAFKGFRNSPVGINHRLRGSLTAIKTRTPQLGGSFAVWG

Parental  GLFSTIDCSMVQIRGKEDPWNSITSGALTGAILAARNGPVAMVGSAAMGGILLALIEGAGILLTRFASAQ
          GLFSTIDCSMVQIRGKEDPWNSITSGALTGAILAARNGPVAMVGSAAMG.ILLALIEGAGILLTRFASAQ
Retrocopy GLFSTIDCSMVQIRGKEDPWNSITSGALTGAILAARNGPVAMVGSAAMGAILLALIEGAGILLTRFASAQ

Parental  FPNGPQFTEDHSQLPSSQLPSSPFGDYRQYQ
          FPNGPQF.EDHSQLPSSQLPSS.FGD.RQYQ
Retrocopy FPNGPQFAEDHSQLPSSQLPSSLFGDHRQYQ

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	0.12 RPM	24.74 RPM
SRP007412_cerebellum	0.04 RPM	19.06 RPM
SRP007412_heart	0.19 RPM	77.27 RPM
SRP007412_kidney	0.38 RPM	45.72 RPM
SRP007412_liver	0.05 RPM	16.14 RPM
SRP007412_testis	0.18 RPM	25.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3045 was not detected

EST

No EST(s) were mapped for retro_mmus_3045 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_137603	84 libraries	47 libraries	689 libraries	224 libraries	28 libraries

The graphical summary, for retro_mmus_3045 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_3045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3045 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012030	4 retrocopies	retro_amel_1667, retro_amel_554, retro_amel_597, retro_amel_622,
Bos taurus	ENSBTAG00000047059	3 retrocopies	retro_btau_1098, retro_btau_1590, retro_btau_872,
Canis familiaris	ENSCAFG00000010612	1 retrocopy	retro_cfam_646,
Choloepus hoffmanni	ENSCHOG00000007440	7 retrocopies	retro_chof_1346, retro_chof_1452, retro_chof_1693, retro_chof_1824, retro_chof_1849, retro_chof_375, retro_chof_435,
Callithrix jacchus	ENSCJAG00000005709	1 retrocopy	retro_cjac_1651,
Dasypus novemcinctus	ENSDNOG00000006389	7 retrocopies	retro_dnov_1113, retro_dnov_1420, retro_dnov_1806, retro_dnov_2586, retro_dnov_273, retro_dnov_274, retro_dnov_814,
Dipodomys ordii	ENSDORG00000013467	4 retrocopies	retro_dord_160, retro_dord_170, retro_dord_536, retro_dord_76,
Equus caballus	ENSECAG00000021816	6 retrocopies	retro_ecab_1036, retro_ecab_1044, retro_ecab_262, retro_ecab_611, retro_ecab_901, retro_ecab_909,
Echinops telfairi	ENSETEG00000006334	6 retrocopies	retro_etel_1179, retro_etel_1356, retro_etel_1809, retro_etel_1958, retro_etel_2211, retro_etel_820,
Homo sapiens	ENSG00000134375	1 retrocopy	retro_hsap_279,
Loxodonta africana	ENSLAFG00000017314	1 retrocopy	retro_lafr_724,
Myotis lucifugus	ENSMLUG00000006569	1 retrocopy	retro_mluc_585,
Macaca mulatta	ENSMMUG00000001924	1 retrocopy	retro_mmul_562,
Monodelphis domestica	ENSMODG00000000517	2 retrocopies	retro_mdom_1007, retro_mdom_381,
Mustela putorius furo	ENSMPUG00000010908	3 retrocopies	retro_mputfur_1455, retro_mputfur_318, retro_mputfur_598,
Mus musculus	ENSMUSG00000031158	1 retrocopy	retro_mmus_1509,
Mus musculus	ENSMUSG00000062580	1 retrocopy	retro_mmus_3045 ,
Nomascus leucogenys	ENSNLEG00000018089	1 retrocopy	retro_nleu_1490,
Oryctolagus cuniculus	ENSOCUG00000007498	3 retrocopies	retro_ocun_1293, retro_ocun_493, retro_ocun_651,
Otolemur garnettii	ENSOGAG00000006176	1 retrocopy	retro_ogar_77,
Pongo abelii	ENSPPYG00000000356	1 retrocopy	retro_pabe_390,
Pan troglodytes	ENSPTRG00000001842	2 retrocopies	retro_ptro_232, retro_ptro_671,
Rattus norvegicus	ENSRNOG00000007040	1 retrocopy	retro_rnor_1417,
Sorex araneus	ENSSARG00000008807	1 retrocopy	retro_sara_270,
Tupaia belangeri	ENSTBEG00000010939	7 retrocopies	retro_tbel_1882, retro_tbel_2869, retro_tbel_2940, retro_tbel_3759, retro_tbel_4197, retro_tbel_4387, retro_tbel_749,
Tarsius syrichta	ENSTSYG00000011606	6 retrocopies	retro_tsyr_1396, retro_tsyr_1512, retro_tsyr_1631, retro_tsyr_1777, retro_tsyr_1920, retro_tsyr_447,
Tursiops truncatus	ENSTTRG00000005973	4 retrocopies	retro_ttru_1044, retro_ttru_1527, retro_ttru_197, retro_ttru_368,