RetrogeneDB ID: retro_mmus_565

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:62702195..62702596(+)
• Located in intron of: ENSMUSG00000036923

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nhp2
• Ensembl ID: ENSMUSG00000001056
• Aliases: Nhp2, 2410130M07Rik, D11Ertd175e, Nola2
• Description: NHP2 ribonucleoprotein [Source:MGI Symbol;Acc:MGI:1098547]

Sequence

>retro_mmus_565
GAGGAGGGCTGCCCCCAGGAGCTGCTGGTCAACCCGAACCCCATCGCGCAGCCCCTGGCTTCCTGCCGCCTGACACGCAA
GCTCTACAAGTCTGTCAAGAAGGCTGTGAAGCAGAAGCAGATTCGTCGTGGAGGGAAGGGGGTTCAGAAATTTGTCAACA
AGGGCATGAAAGGGATCATGGTTTTGGCAGGAGATACATTGTGGATTGAAGTGTACTGCCATCTTCCAATTCTGTGTGAG
GACCAGAACTTGCCCTATGTCTACGTCCCTCTAAGACAGACGTGGGTGCAGCCACAGGCTACAAGCGTCCCACTTGTGTG
ATCATGGTGAAGCCCCATGAAGGATATCAGGAGGCCCACGACAAGTGCCTGGAGGAGGTGCAGGCACTGCCTACACCTCT
G

Alignment

ORF - retro_mmus_565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 87.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EERTYKELLVNLNPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIE
          EE....ELLVN.NPIAQPLAS.RLTRKLYK..KKAVKQKQIRRG.K.VQKFVNKG.KGIMVLAGDTL.IE
Retrocopy EEGCPQELLVNPNPIAQPLASCRLTRKLYKSVKKAVKQKQIRRGGKGVQKFVNKGMKGIMVLAGDTLWIE

Parental  VYCHLPVLCEDQNLPYVYI-PSKTDLGAATGSKRPTCVIMVKPHEEYQETYDKCLEEVQALPTPL
          VYCHLP.LCEDQNLPYVY..PSKTD.GAATG.KRPTCVIMVKPHE.YQE..DKCLEEVQALPTPL
Retrocopy VYCHLPILCEDQNLPYVYV<PSKTDVGAATGYKRPTCVIMVKPHEGYQEAHDKCLEEVQALPTPL

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	15.44 RPM
SRP007412_cerebellum	0.00 RPM	10.51 RPM
SRP007412_heart	0.00 RPM	14.04 RPM
SRP007412_kidney	0.00 RPM	21.52 RPM
SRP007412_liver	0.00 RPM	18.76 RPM
SRP007412_testis	6.86 RPM	16.74 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_565 was not detected

EST

No EST(s) were mapped for retro_mmus_565 retrocopy.

TSS

No TSS is located nearby retro_mmus_565 retrocopy 5' end.

Lab

retro_mmus_565 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_565 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012244	1 retrocopy	retro_cjac_264,
Homo sapiens	ENSG00000145912	2 retrocopies	retro_hsap_3712, retro_hsap_611,
Gorilla gorilla	ENSGGOG00000000015	1 retrocopy	retro_ggor_2509,
Macropus eugenii	ENSMEUG00000003839	2 retrocopies	retro_meug_285, retro_meug_320,
Macaca mulatta	ENSMMUG00000018757	1 retrocopy	retro_mmul_1702,
Monodelphis domestica	ENSMODG00000004231	1 retrocopy	retro_mdom_345,
Mus musculus	ENSMUSG00000001056	1 retrocopy	retro_mmus_565 ,
Oryctolagus cuniculus	ENSOCUG00000016057	1 retrocopy	retro_ocun_151,
Ochotona princeps	ENSOPRG00000007907	3 retrocopies	retro_opri_305, retro_opri_421, retro_opri_810,
Pongo abelii	ENSPPYG00000016105	3 retrocopies	retro_pabe_1704, retro_pabe_3143, retro_pabe_481,
Rattus norvegicus	ENSRNOG00000004247	2 retrocopies	retro_rnor_1436, retro_rnor_2198,
Sus scrofa	ENSSSCG00000014032	1 retrocopy	retro_sscr_407,