RetrogeneDB ID: retro_mmus_2

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:59395754..59396384(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000069622
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Timm23
• Ensembl ID: ENSMUSG00000013701
• Aliases: Timm23, Tim23
• Description: translocase of inner mitochondrial membrane 23 [Source:MGI Symbol;Acc:MGI:1858317]

Sequence

>retro_mmus_2
ATGGAAGGTGGCGGAGGAAGTAGCAACAAATCCACCAGCGGGTTAGCTGGCTTCTTCGGAGCCGGAGGAGCGGGTTACTC
GAACGCTGATTTGGCCGGCGTCCCGCTGACTGGTATGAACCCCCTGTCTCCTTATTTAAATGTGGATCCACGCTATCTCG
TTCAGGATACTGATGAATTTATTTTGCCAACTGGAGCTAATAAAACCCGAGGCAGATTTGAACTAGCTTTCTTTACCATT
GGAGGATGTTGCATGACAGGGGCCGCATTCGGGGCAATGAACGGTCTTCGTTTAGGATTGAAGGAAACCCAGAGCATGGC
CTGGTCCAAACCAAGAAATGTACAGATTTTGAATATGGTGACTAGGCAAGGAGCACTTTGGGCTAATACTCTAGGCTCCC
TGGCTTTGCTCTATAGTGCTTTTGGTGTTATCATTGAGAAAACACGGGGTGCAGAAGATGACCTCAACACAGTAGCAGCT
GGAACCATGACCGGGATGTTGTATAAATGTACAGGTGGTCTTCGAGGAATAGCACGCGGTGGCCTGGCAGGACTGACACT
CACCAGTCTCTATGCACTGTATAACAACTGGGAGCACATGAAAGGTTCCCTGCTCCAACAGTCACTCTGA

Alignment

ORF - retro_mmus_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGGGGSSNKSTSGLAGFFGAGGAGYSNADLAGVPLTGMNPLSPYLNVDPRYLVQDTDEFILPTGANKTR
          MEGGGGSSNKSTSGLAGFFGAGGAGYSNADLAGVPLTGMNPLSPYLNVDPRYLVQDTDEFILPTGANKTR
Retrocopy MEGGGGSSNKSTSGLAGFFGAGGAGYSNADLAGVPLTGMNPLSPYLNVDPRYLVQDTDEFILPTGANKTR

Parental  GRFELAFFTIGGCCMTGAAFGAMNGLRLGLKETQSMAWSKPRNVQILNMVTRQGALWANTLGSLALLYSA
          GRFELAFFTIGGCCMTGAAFGAMNGLRLGLKETQSMAWSKPRNVQILNMVTRQGALWANTLGSLALLYSA
Retrocopy GRFELAFFTIGGCCMTGAAFGAMNGLRLGLKETQSMAWSKPRNVQILNMVTRQGALWANTLGSLALLYSA

Parental  FGVIIEKTRGAEDDLNTVAAGTMTGMLYKCTGGLRGIARGGLAGLTLTSLYALYNNWEHMKGSLLQQSL
          FGVIIEKTRGAEDDLNTVAAGTMTGMLYKCTGGLRGIARGGLAGLTLTSLYALYNNWEHMKGSLLQQSL
Retrocopy FGVIIEKTRGAEDDLNTVAAGTMTGMLYKCTGGLRGIARGGLAGLTLTSLYALYNNWEHMKGSLLQQSL

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	2.76 RPM
SRP007412_cerebellum	0.00 RPM	2.26 RPM
SRP007412_heart	0.00 RPM	13.20 RPM
SRP007412_kidney	0.00 RPM	4.16 RPM
SRP007412_liver	0.00 RPM	4.04 RPM
SRP007412_testis	0.00 RPM	2.42 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2 was not detected

EST

No EST(s) were mapped for retro_mmus_2 retrocopy.

TSS

No TSS is located nearby retro_mmus_2 retrocopy 5' end.

Lab

retro_mmus_2 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007501	1 retrocopy	retro_amel_1488,
Canis familiaris	ENSCAFG00000029477	1 retrocopy	retro_cfam_329,
Choloepus hoffmanni	ENSCHOG00000007073	1 retrocopy	retro_chof_797,
Callithrix jacchus	ENSCJAG00000013336	1 retrocopy	retro_cjac_2965,
Cavia porcellus	ENSCPOG00000019917	2 retrocopies	retro_cpor_1013, retro_cpor_321,
Monodelphis domestica	ENSMODG00000002661	2 retrocopies	retro_mdom_1202, retro_mdom_860,
Mus musculus	ENSMUSG00000013701	1 retrocopy	retro_mmus_2 ,
Oryctolagus cuniculus	ENSOCUG00000000525	1 retrocopy	retro_ocun_73,
Otolemur garnettii	ENSOGAG00000015393	1 retrocopy	retro_ogar_2627,
Ochotona princeps	ENSOPRG00000005255	2 retrocopies	retro_opri_520, retro_opri_920,
Procavia capensis	ENSPCAG00000015914	1 retrocopy	retro_pcap_181,
Rattus norvegicus	ENSRNOG00000019811	3 retrocopies	retro_rnor_1804, retro_rnor_225, retro_rnor_661,
Sorex araneus	ENSSARG00000010335	1 retrocopy	retro_sara_86,
Sus scrofa	ENSSSCG00000025276	1 retrocopy	retro_sscr_404,
Ictidomys tridecemlineatus	ENSSTOG00000007041	1 retrocopy	retro_itri_1043,