RetrogeneDB ID: retro_mmus_73

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:43524167..43524545(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000045886
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Pam16
• Ensembl ID: ENSMUSG00000014301
• Aliases: Pam16, 2010110I09Rik, AV006767, CGI-136, Magmas, Tim16, Timm16
• Description: presequence translocase-asssociated motor 16 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913699]

Sequence

>retro_mmus_73
ATGGCCAAGTACCTGGCCCAGATCATTGTGATGGGTGTGCAGGTGGTGGGCAGAGCCTTTGCCAGGGCCCTGAGGCAGGA
GTTTGCAGCCAGCCAGGCAGCCGCTGACGCTCGAGGGCGTGCTGGGCACCAGTCTGCAGCTGCATCCAATCTCTCTGGCC
TCAGCCTCCAGGAAGCCCAGCAGATTCTCAACGTCTCCAAGCTGAGCCCCGAGGAGGTCCAGAAGAATTATGAACACCTA
TTTAAAGTGAATGATAAGTCCGTGGGTGGCTCTTTCTACCTGCAGTCAAAGGTTGTCCGTGCAAAGGAACGTCTAGATGA
GGAACTCCGAATACAAGCCCAGGAAGACAGAGAGAAAGGGCAGAAGCCCAAAACGTGA

Alignment

ORF - retro_mmus_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAKYLAQIIVMGVQVVGRAFARALRQEFAASQAAADARGRAGHQSAAASNLSGLSLQEAQQILNVSKLSP
          MAKYLAQIIVMGVQVVGRAFARALRQEFAASQAAADARGRAGHQSAAASNLSGLSLQEAQQILNVSKLSP
Retrocopy MAKYLAQIIVMGVQVVGRAFARALRQEFAASQAAADARGRAGHQSAAASNLSGLSLQEAQQILNVSKLSP

Parental  EEVQKNYEHLFKVNDKSVGGSFYLQSKVVRAKERLDEELRIQAQEDREKGQKPKT
          EEVQKNYEHLFKVNDKSVGGSFYLQSKVVRAKERLDEELRIQAQEDREKGQKPKT
Retrocopy EEVQKNYEHLFKVNDKSVGGSFYLQSKVVRAKERLDEELRIQAQEDREKGQKPKT

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	0.07 RPM	5.84 RPM
SRP007412_cerebellum	0.00 RPM	4.95 RPM
SRP007412_heart	0.25 RPM	9.68 RPM
SRP007412_kidney	0.08 RPM	8.89 RPM
SRP007412_liver	0.00 RPM	5.33 RPM
SRP007412_testis	0.27 RPM	19.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_73 was not detected

EST

No EST(s) were mapped for retro_mmus_73 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_3399	452 libraries	106 libraries	430 libraries	75 libraries	9 libraries
TSS #2	TSS_3400	106 libraries	236 libraries	614 libraries	108 libraries	8 libraries

The graphical summary, for retro_mmus_73 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_73 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_73 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73 ,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,