RetrogeneDB ID: retro_mmus_282

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:107414140..107414737(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000049233
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Apoo
• Ensembl ID: ENSMUSG00000079508
• Aliases: Apoo, 0610008C08Rik, 1110019O03Rik
• Description: apolipoprotein O [Source:MGI Symbol;Acc:MGI:1915566]

Sequence

>retro_mmus_282
ATGTTCAAGGTAATTCAGAGATCTGTGGGGCCAGCCAGCCTGAGCCTGCTCACCTTCAGAGTCTATGCAGCACCCAAAAA
GGACTCGCCTCACAAAAGTTACATGAAGATCGATGAGCTTTCACTCTACTCAGTTCCTGAGGGTCAATCTAAATATGTGG
AGGAGCCAAGGACTCAACTTGAAGAAAACATCTCACAACTCCGACATCATTGTGAGCCATATACAAGTTTCTGTCAGGAA
ATATACTCCCATACTAAACCCAAGGTGGATCACTTTGTCCAGTGGGGAGTAGACAACTATAACTATCTTCAAAATGCGCC
TCCTGGATTTTTCCCAAGACTCGGTGTTATTGGTTTTGCTGGTTTTGTTGGACTCCTTTTTGCTAGAGGTTCAAAAATAA
AGAAGCTGGTGTATCCTCCTTTTTTCATGGGATTAGGTGCCTCTGTCTATTACCCACAACAAGCCATCACCATTGCCCAG
ATCACTGGGGAGAAGTTATATGACTGGGGATTACGAGGGTACATAGTTATAGAAGATTTGTGGAAGCAAAATTTTCAGAA
GCCAGGAAATGTGAAGAATTCACCTGGAAATAAATAG

Alignment

ORF - retro_mmus_282 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  MFKVIQRSVGPASLSLLTFRVYAAPKKDSPHKSYMKIDELSLYSVPEGQSKYVEEPRTQLEENISQLRHH
          MFKVIQRSVGPASLSLLTFRVYAAPKKDSPHKSYMKIDELSLYSVPEGQSKYVEEPRTQLEENISQLRHH
Retrocopy MFKVIQRSVGPASLSLLTFRVYAAPKKDSPHKSYMKIDELSLYSVPEGQSKYVEEPRTQLEENISQLRHH

Parental  CEPYTSFCQEIYSHTKPKVDHFVQWGVDNYNYLQNAPPGFFPRLGVIGFAGFVGLLFARGSKIKKLVYPP
          CEPYTSFCQEIYSHTKPKVDHFVQWGVDNYNYLQNAPPGFFPRLGVIGFAGFVGLLFARGSKIKKLVYPP
Retrocopy CEPYTSFCQEIYSHTKPKVDHFVQWGVDNYNYLQNAPPGFFPRLGVIGFAGFVGLLFARGSKIKKLVYPP

Parental  FFMGLGASVYYPQQAITIAQITGEKLYDWGLRGYIVIEDLWKQNFQKPGNVKNSPGNK
          FFMGLGASVYYPQQAITIAQITGEKLYDWGLRGYIVIEDLWKQNFQKPGNVKNSPGNK
Retrocopy FFMGLGASVYYPQQAITIAQITGEKLYDWGLRGYIVIEDLWKQNFQKPGNVKNSPGNK

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	1.94 RPM
SRP007412_cerebellum	0.35 RPM	0.78 RPM
SRP007412_heart	0.56 RPM	5.63 RPM
SRP007412_kidney	0.94 RPM	3.64 RPM
SRP007412_liver	0.16 RPM	0.90 RPM
SRP007412_testis	0.23 RPM	0.64 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_282 was not detected

EST

No EST(s) were mapped for retro_mmus_282 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_26441	112 libraries	79 libraries	725 libraries	137 libraries	19 libraries

The graphical summary, for retro_mmus_282 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_282 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_282 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012749	1 retrocopy	retro_amel_1282,
Choloepus hoffmanni	ENSCHOG00000000226	2 retrocopies	retro_chof_2372, retro_chof_839,
Callithrix jacchus	ENSCJAG00000004909	8 retrocopies	retro_cjac_1360, retro_cjac_1417, retro_cjac_1448, retro_cjac_1767, retro_cjac_1792, retro_cjac_1896, retro_cjac_2038, retro_cjac_2063,
Cavia porcellus	ENSCPOG00000004197	1 retrocopy	retro_cpor_309,
Dasypus novemcinctus	ENSDNOG00000006710	1 retrocopy	retro_dnov_2450,
Equus caballus	ENSECAG00000013441	1 retrocopy	retro_ecab_145,
Echinops telfairi	ENSETEG00000014150	3 retrocopies	retro_etel_1052, retro_etel_516, retro_etel_711,
Felis catus	ENSFCAG00000000029	3 retrocopies	retro_fcat_1203, retro_fcat_1657, retro_fcat_1798,
Homo sapiens	ENSG00000184831	5 retrocopies	retro_hsap_1018, retro_hsap_1693, retro_hsap_2670, retro_hsap_3047, retro_hsap_3259,
Gorilla gorilla	ENSGGOG00000001200	4 retrocopies	retro_ggor_1269, retro_ggor_1863, retro_ggor_2098, retro_ggor_806,
Loxodonta africana	ENSLAFG00000029070	1 retrocopy	retro_lafr_1114,
Macropus eugenii	ENSMEUG00000014222	1 retrocopy	retro_meug_700,
Macaca mulatta	ENSMMUG00000016361	4 retrocopies	retro_mmul_1584, retro_mmul_1886, retro_mmul_2051, retro_mmul_814,
Monodelphis domestica	ENSMODG00000025554	1 retrocopy	retro_mdom_1510,
Mustela putorius furo	ENSMPUG00000000109	1 retrocopy	retro_mputfur_109,
Mus musculus	ENSMUSG00000079508	1 retrocopy	retro_mmus_282 ,
Nomascus leucogenys	ENSNLEG00000010026	5 retrocopies	retro_nleu_1167, retro_nleu_1338, retro_nleu_1944, retro_nleu_456, retro_nleu_898,
Otolemur garnettii	ENSOGAG00000001960	6 retrocopies	retro_ogar_1083, retro_ogar_1104, retro_ogar_2092, retro_ogar_2466, retro_ogar_2927, retro_ogar_3094,
Pongo abelii	ENSPPYG00000020191	7 retrocopies	retro_pabe_1394, retro_pabe_1417, retro_pabe_2215, retro_pabe_2417, retro_pabe_2434, retro_pabe_2702, retro_pabe_856,
Pan troglodytes	ENSPTRG00000021742	5 retrocopies	retro_ptro_1147, retro_ptro_1799, retro_ptro_1992, retro_ptro_2205, retro_ptro_746,
Pteropus vampyrus	ENSPVAG00000002530	2 retrocopies	retro_pvam_128, retro_pvam_594,
Rattus norvegicus	ENSRNOG00000046918	4 retrocopies	retro_rnor_1022, retro_rnor_1986, retro_rnor_2096, retro_rnor_2308,
Sarcophilus harrisii	ENSSHAG00000008734	1 retrocopy	retro_shar_125,
Sus scrofa	ENSSSCG00000012174	1 retrocopy	retro_sscr_774,
Tupaia belangeri	ENSTBEG00000014888	6 retrocopies	retro_tbel_1153, retro_tbel_4004, retro_tbel_4261, retro_tbel_4698, retro_tbel_715, retro_tbel_96,
Tarsius syrichta	ENSTSYG00000010239	2 retrocopies	retro_tsyr_1089, retro_tsyr_2155,