RetrogeneDB ID: retro_mmus_2579

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:75108634..75108888(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufa2
• Ensembl ID: ENSMUSG00000014294
• Aliases: Ndufa2, AV000592, B8, C1-B8, CI-B8
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 [Source:MGI Symbol;Acc:MGI:1343103]

Sequence

>retro_mmus_2579
ATGGCAGTCACCGCTGTTAGCCGAGTGGTCGGTGCAAAGCTGGGGCTGTGTGAGACTCGCATTCACTTATGCCAGCGTTC
CTCCCCCAGGCAGGGCAAGGATGTGAGGAATTTCATGCTGCAATGGCGTGTGGAGTGAAGGATGAGCACTCCGACCTGCC
CATTCTAATCCGCTAATGTTCGGAGGTGCAGCCCAAGCTCTGGGCCGGCTATGCTTTTGGCCAAGAGAACAATCTGAGTG
CTGATGAGGTAACC

Alignment

ORF - retro_mmus_2579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.63 %
• Parental protein coverage: 83.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAAASRAVGAKLGLREIRVHLCQRSPGSQG--VRDFIVQRYVE-LKKAHPNLPILIRECSEVQPKLWA
          MA..A.SR.VGAKLGL.E.R.HLCQRS...QG..VR.F..Q..VE..K..H..LPILIR.CSEVQPKLWA
Retrocopy MAVTAVSRVVGAKLGLCETRIHLCQRSSPRQGKDVRNFMLQWRVE<VKDEHSDLPILIR*CSEVQPKLWA

Parental  RYAFGQEKTVSLNNLS
          .YAFGQE...S.....
Retrocopy GYAFGQENNLSADEVT

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	0.02 RPM	46.28 RPM
SRP007412_cerebellum	0.00 RPM	40.90 RPM
SRP007412_heart	0.00 RPM	156.21 RPM
SRP007412_kidney	0.00 RPM	95.63 RPM
SRP007412_liver	0.00 RPM	62.29 RPM
SRP007412_testis	0.05 RPM	52.10 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2579 was not detected

EST

No EST(s) were mapped for retro_mmus_2579 retrocopy.

TSS

No TSS is located nearby retro_mmus_2579 retrocopy 5' end.

Lab

retro_mmus_2579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015041	2 retrocopies	retro_btau_124, retro_btau_151,
Canis familiaris	ENSCAFG00000005861	1 retrocopy	retro_cfam_1343,
Callithrix jacchus	ENSCJAG00000016525	1 retrocopy	retro_cjac_3326,
Cavia porcellus	ENSCPOG00000009178	2 retrocopies	retro_cpor_1045, retro_cpor_1290,
Latimeria chalumnae	ENSLACG00000005796	1 retrocopy	retro_lcha_48,
Mus musculus	ENSMUSG00000014294	1 retrocopy	retro_mmus_2579 ,
Nomascus leucogenys	ENSNLEG00000009325	1 retrocopy	retro_nleu_67,
Otolemur garnettii	ENSOGAG00000027727	1 retrocopy	retro_ogar_1633,
Pongo abelii	ENSPPYG00000015860	1 retrocopy	retro_pabe_938,
Rattus norvegicus	ENSRNOG00000017571	1 retrocopy	retro_rnor_262,
Sus scrofa	ENSSSCG00000014371	1 retrocopy	retro_sscr_48,
Tupaia belangeri	ENSTBEG00000005978	1 retrocopy	retro_tbel_2688,