RetrogeneDB ID: retro_mmus_2693

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:117294031..117294367(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufa6
• Ensembl ID: ENSMUSG00000022450
• Aliases: Ndufa6, 14kDa, 2700038D15Rik, B230217P19Rik
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14) [Source:MGI Symbol;Acc:MGI:1914380]

Sequence

>retro_mmus_2693
GTGAAGCCCATTTCCAGTCGTGACCCGAGGAGGCCAAGCAGAGGGTGCGCGAACTCTACCGCGCTCGGTATCCGGAGGTG
CCGAACACTGTGCACTTAATGCACCTGGATAGCATGGTGAAACAAGGACAGGAGAAAGTCTGAGAAATGAACATGCAAAA
TGCCCATGTCACAGACCCCAGAGTGGTTGCTTTCCTGGTCACTAAGGGAAAAGTTGGAGCTCCAGGAAAACATTAAAGTA
TGGAAGCAGCGGACACACGTTATGTGGGTTTTCCAGGAAACAGAAACACCAAGGCTAAAGGATTTCTTGTCTAAGTTCTA
TGTTGGCCATGACCCA

Alignment

ORF - retro_mmus_2693 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.19 %
• Parental protein coverage: 85.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKPIFSRDLN-EAKRRVRELYRAWYREVPNTVHLMQLDITVKQGRDKVREMFMKNAHVTDPRVVDLLVIK
          VKPI.SRD...EAK.RVRELYRA.Y.EVPNTVHLM.LD..VKQG..KV.EM.M.NAHVTDPRVV..LV.K
Retrocopy VKPISSRDPR<EAKQRVRELYRARYPEVPNTVHLMHLDSMVKQGQEKV*EMNMQNAHVTDPRVVAFLVTK

Parental  G-KMELQETIKVWKQRTHVMRFFHETETPRPKDFLSKFYMGHDP
          G.K.ELQE.IKVWKQRTHVM..F.ETETPR.KDFLSKFY.GHDP
Retrocopy G>KLELQENIKVWKQRTHVMWVFQETETPRLKDFLSKFYVGHDP

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	0.05 RPM	54.79 RPM
SRP007412_cerebellum	0.00 RPM	71.12 RPM
SRP007412_heart	0.00 RPM	173.33 RPM
SRP007412_kidney	0.00 RPM	163.99 RPM
SRP007412_liver	0.00 RPM	137.42 RPM
SRP007412_testis	0.14 RPM	60.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2693 was not detected

EST

No EST(s) were mapped for retro_mmus_2693 retrocopy.

TSS

No TSS is located nearby retro_mmus_2693 retrocopy 5' end.

Lab

retro_mmus_2693 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2693 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000001466	1 retrocopy	retro_csav_29,
Erinaceus europaeus	ENSEEUG00000004117	1 retrocopy	retro_eeur_664,
Monodelphis domestica	ENSMODG00000007030	1 retrocopy	retro_mdom_397,
Mus musculus	ENSMUSG00000022450	1 retrocopy	retro_mmus_2693 ,
Oryctolagus cuniculus	ENSOCUG00000015446	1 retrocopy	retro_ocun_1128,
Otolemur garnettii	ENSOGAG00000014762	2 retrocopies	retro_ogar_1656, retro_ogar_312,
Procavia capensis	ENSPCAG00000004570	1 retrocopy	retro_pcap_18,
Rattus norvegicus	ENSRNOG00000008569	1 retrocopy	retro_rnor_604,
Sorex araneus	ENSSARG00000003814	1 retrocopy	retro_sara_75,