RetrogeneDB ID: retro_mmus_1469

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:55074413..55074880(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Chmp5
• Ensembl ID: ENSMUSG00000028419
• Aliases: Chmp5, 2210412K09Rik, AW545668
• Description: charged multivesicular body protein 5 [Source:MGI Symbol;Acc:MGI:1924209]

Sequence

>retro_mmus_1469
CCCAAGGCTCTTCCACCCAGCCTGACTGACTGCATTTGGGACAGTGAATAGCAGGGGCAGTATCCATTGACAAAAAGATT
TCCCAGTTAGATGTTGAACTAGCGAAATATAAGTATTAAATCAAGAACATGAGAGAGGGTCCTTCGAAGAACATGGTCAA
ACAGAAAGCCCTGAGGGTTTTAAAGCAAAAGCAAATGTATGAGAAGCAGTGAGACAACCTTGCCTCACAGTCCTTTGACA
TGGAGCAAGCTAATTACACCATCCAGTCACTGAAGGACACCAAGACCATGGTTGATGCCATGAAATTGGGAGTAAAAGAA
GTGAAGAAGGCATACAAGGAAGTGAAAATTGACCAGATTGAGGATTTACAAGACCAGCTGGAAGATCGGAAAGAAGAGAC
AAACGAGATCCAGGAAGCACTGAGCCTCAGCTTTGACACCTCAGAATTAGATGAGAATAACCTGGAA

Alignment

ORF - retro_mmus_1469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.89 %
• Parental protein coverage: 70.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKAPPPSLTDCI-GTVDSR-AESIDKKISRLDAELVKYKDQIKKMREGPAKNMVKQKALRVLKQKRMYEQ
          PKA.PPSLTDCI.GTV.SR.A.SIDKKIS.LD.EL.KYK..IK.MREGP.KNMVKQKALRVLKQK.MYE.
Retrocopy PKALPPSLTDCI>GTVNSR>AVSIDKKISQLDVELAKYKY*IKNMREGPSKNMVKQKALRVLKQKQMYEK

Parental  QRDNLAQQSFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKEVKIDQIEDLQDQLEDMMEDANEIQE
          Q.DNLA.QSF.MEQANYTIQSLKDTKT.VDAMKLGVKE.KKAYKEVKIDQIEDLQDQLED..E..NEIQE
Retrocopy Q*DNLASQSFDMEQANYTIQSLKDTKTMVDAMKLGVKEVKKAYKEVKIDQIEDLQDQLEDRKEETNEIQE

Parental  ALGRSYGTPELDEDDLE
          AL..S..T.ELDE..LE
Retrocopy ALSLSFDTSELDENNLE

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	50.39 RPM
SRP007412_cerebellum	0.00 RPM	62.74 RPM
SRP007412_heart	0.00 RPM	29.29 RPM
SRP007412_kidney	0.00 RPM	75.59 RPM
SRP007412_liver	0.00 RPM	46.18 RPM
SRP007412_testis	0.00 RPM	39.79 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1469 was not detected

EST

No EST(s) were mapped for retro_mmus_1469 retrocopy.

TSS

No TSS is located nearby retro_mmus_1469 retrocopy 5' end.

Lab

retro_mmus_1469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1469 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012672	1 retrocopy	retro_chof_2045,
Callithrix jacchus	ENSCJAG00000008104	2 retrocopies	retro_cjac_2868, retro_cjac_4159,
Cavia porcellus	ENSCPOG00000003467	2 retrocopies	retro_cpor_1221, retro_cpor_1306,
Dipodomys ordii	ENSDORG00000006280	2 retrocopies	retro_dord_292, retro_dord_764,
Echinops telfairi	ENSETEG00000001424	1 retrocopy	retro_etel_2126,
Homo sapiens	ENSG00000086065	2 retrocopies	retro_hsap_4822, retro_hsap_494,
Microcebus murinus	ENSMICG00000012113	2 retrocopies	retro_mmur_369, retro_mmur_843,
Myotis lucifugus	ENSMLUG00000011045	1 retrocopy	retro_mluc_954,
Macaca mulatta	ENSMMUG00000020149	1 retrocopy	retro_mmul_2573,
Monodelphis domestica	ENSMODG00000004012	2 retrocopies	retro_mdom_2002, retro_mdom_595,
Mus musculus	ENSMUSG00000028419	1 retrocopy	retro_mmus_1469 ,
Nomascus leucogenys	ENSNLEG00000005158	2 retrocopies	retro_nleu_2197, retro_nleu_2420,
Otolemur garnettii	ENSOGAG00000000774	6 retrocopies	retro_ogar_2072, retro_ogar_2190, retro_ogar_2386, retro_ogar_2504, retro_ogar_2509, retro_ogar_916,
Pongo abelii	ENSPPYG00000019137	2 retrocopies	retro_pabe_239, retro_pabe_3750,
Pan troglodytes	ENSPTRG00000020857	2 retrocopies	retro_ptro_3210, retro_ptro_373,
Rattus norvegicus	ENSRNOG00000008672	1 retrocopy	retro_rnor_2614,
Ictidomys tridecemlineatus	ENSSTOG00000026573	1 retrocopy	retro_itri_424,
Tupaia belangeri	ENSTBEG00000003486	5 retrocopies	retro_tbel_1626, retro_tbel_1894, retro_tbel_2407, retro_tbel_3364, retro_tbel_3494,
Tursiops truncatus	ENSTTRG00000010575	1 retrocopy	retro_ttru_338,