RetrogeneDB ID: retro_mmur_420

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_2940:178671..179272(+)
• Located in intron of: ENSMICG00000005441

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM40
• Ensembl ID: ENSMICG00000014041
• Aliases: None
• Description: translocase of outer mitochondrial membrane 40 homolog (yeast) [Source:HGNC Symbol;Acc:18001]

Sequence

>retro_mmur_420
TTCCCCACTGTGGTTGGTGACAGTGACAGCAGTGGCAGCCTTAATGCCCTGTTTCTGCTCCTCTTGGCAGAGCAGCTCCG
AGCTAAGGCTGTCTTCCAGATGCAGCAGGCCAAGTTCCCGACATGGCAGTTTCATTGAGAGTGTCAGGGAGATGACTACA
CAGACATTCTGACCCTAGGAAATCCTGACCTGATTGGGGAATTGGTGATCATGGTCCCTTACTTCCTGCAGAGCTTCACT
CTTTGGCTAGTGCTGGGAGGAGAGCCAGTTTATCACTGGTGGCCGGGTAAAGAGGGGGTCAACTTGACAGTGGCTGGGAA
ATACTTGGCTGTATACTGGGTAGCTGCATTGAATATGGGACCAGGCAGAGGCCATGCGAGTGATTATCACAGGGCAAAGG
AACAGGTTTAGGCTGGAGTGGAGTTTGAAGTAAACGCAAGGCTACATGTCACAACCTTTTCCTTTGGTTACCACCTGACT
TTGCTCCAGGCCAACATGGTGTTTAGAGGCTTAGTGGATAGTAACTGGTGTGTAGGTGCTATGCTGGAGAAGAAGATGAC
CCCCCTTGCCTGTCACCCTTGCTCTTGGAGCCTTCCTTAAT

Alignment

ORF - retro_mmur_420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.24 %
• Parental protein coverage: 55.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFTAAVTLGNPDVLVGSGI
          FP..VGD.D.SGSLNA.....L...LR.K...Q.QQ.KF..WQ...E..G.D.T...TLGNPD......I
Retrocopy FPTVVGDSDSSGSLNALFLLLLAEQLRAKAVFQMQQAKFPTWQFH*ECQGDDYTDILTLGNPDLIGELVI

Parental  LVAHYLQSITPCLALGGELVYRRRPGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGV
          .V...LQS.T..L.LGGE.VY...PG.EG.....AGKY....W.A....G....HA..YH.A..Q...GV
Retrocopy MVPYFLQSFTLWLVLGGEPVYHWWPGKEGVNLTVAGKYLAVYWVAALNMGPGRGHASDYHRAKEQV*AGV

Parental  EFEASTRMQDTSVSFGYQLDLPKANLLFKGSVDSNWIVGATLEKKL-PPLPLTLALGAFLN
          EFE...R...T..SFGY.L.L..AN..F.G.VDSNW.VGA.LEKK..PPLP.TLALGAFLN
Retrocopy EFEVNARLHVTTFSFGYHLTLLQANMVFRGLVDSNWCVGAMLEKKM>PPLPVTLALGAFLN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_420 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_420 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130204	5 retrocopies	retro_hsap_1300, retro_hsap_1386, retro_hsap_2321, retro_hsap_2537, retro_hsap_3159,
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356,
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420 ,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Macaca mulatta	ENSMMUG00000014303	1 retrocopy	retro_mmul_1998,
Nomascus leucogenys	ENSNLEG00000001726	2 retrocopies	retro_nleu_2368, retro_nleu_2542,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,