RetrogeneDB ID: retro_mmus_2571

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:57608566..57609064(+)
• Located in intron of: ENSMUSG00000097216

Retrocopy information

• Ensembl ID: ENSMUSG00000051116
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Immp1l
• Ensembl ID: ENSMUSG00000042670
• Aliases: Immp1l, 1500034J20Rik, 2610528O17Rik, AU042386
• Description: IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913791]

Sequence

>retro_mmus_2571
ATGCTTCGTGGTGTTCTGGGAAAGGCTTTTCGACTTGCTGGCTATACCATTCAGTATGGCTGCATAGCTCATTGTGCTTT
TGAATACGTTGGTGGTGTTGTAATGTGTTCTGGACCATCAATGGAACCCACAATTCAAAATTCAGATATTGTCTTTGCAG
AAAATCTTAGCCGACATTTTTATGGCATCCAAAGAGGTGACATTGTAATTGCAAAAAGCCCAAGTGATCCAAAATCAAAT
ATCTGTAAAAGAGTAATTGGTTTGGAAGGAGACAAAATCCTCAGCACTAGCCCATCTGATGTATTTAAGAGCCGTAGTTA
TGTGCCAACAGGTCATGTTTGGTTAGAAGGTGATAACTTACAGAATTCTACCGATTCCAGGTATTATGGACCTATACCAT
ATGGACTAATAAGAGGACATATCTTCTTTAAGATTTGGCCTTTCAGTGACTTCGGATTTCTGCGTGACAGCCCAAATGGC
CAGAGATCTTCTGATGAT

Alignment

ORF - retro_mmus_2571 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRGVLGKAFRLAGYTIQYGCIAHCAFEYVGGVVMCSGPSMEPTIQNSDIVFAENLSRHFYGIQRGDIVI
          MLRGVLGKAFRLAGYTIQYGCIAHCAFEYVGGVVMCSGPSMEPTIQNSDIVFAENLSRHFYGIQRGDIVI
Retrocopy MLRGVLGKAFRLAGYTIQYGCIAHCAFEYVGGVVMCSGPSMEPTIQNSDIVFAENLSRHFYGIQRGDIVI

Parental  AKSPSDPKSNICKRVIGLEGDKILSTSPSDVFKSRSYVPTGHVWLEGDNLQNSTDSRYYGPIPYGLIRGR
          AKSPSDPKSNICKRVIGLEGDKILSTSPSDVFKSRSYVPTGHVWLEGDNLQNSTDSRYYGPIPYGLIRG.
Retrocopy AKSPSDPKSNICKRVIGLEGDKILSTSPSDVFKSRSYVPTGHVWLEGDNLQNSTDSRYYGPIPYGLIRGH

Parental  IFFKIWPFSDFGFLRDSPNGQRFSDD
          IFFKIWPFSDFGFLRDSPNGQR.SDD
Retrocopy IFFKIWPFSDFGFLRDSPNGQRSSDD

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	0.14 RPM	4.60 RPM
SRP007412_cerebellum	0.09 RPM	3.60 RPM
SRP007412_heart	0.09 RPM	12.45 RPM
SRP007412_kidney	0.12 RPM	7.95 RPM
SRP007412_liver	0.08 RPM	5.19 RPM
SRP007412_testis	0.23 RPM	12.58 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2571 was not detected

EST

No EST(s) were mapped for retro_mmus_2571 retrocopy.

TSS

No TSS is located nearby retro_mmus_2571 retrocopy 5' end.

Lab

retro_mmus_2571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2571 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006876	1 retrocopy	retro_amel_623,
Bos taurus	ENSBTAG00000000475	1 retrocopy	retro_btau_528,
Canis familiaris	ENSCAFG00000007514	2 retrocopies	retro_cfam_1757, retro_cfam_548,
Choloepus hoffmanni	ENSCHOG00000010106	4 retrocopies	retro_chof_1157, retro_chof_1665, retro_chof_2427, retro_chof_358,
Callithrix jacchus	ENSCJAG00000006042	1 retrocopy	retro_cjac_1240,
Dipodomys ordii	ENSDORG00000000250	4 retrocopies	retro_dord_144, retro_dord_205, retro_dord_243, retro_dord_726,
Equus caballus	ENSECAG00000020512	3 retrocopies	retro_ecab_1019, retro_ecab_159, retro_ecab_920,
Echinops telfairi	ENSETEG00000003057	1 retrocopy	retro_etel_1971,
Homo sapiens	ENSG00000148950	1 retrocopy	retro_hsap_786,
Gorilla gorilla	ENSGGOG00000014897	1 retrocopy	retro_ggor_651,
Myotis lucifugus	ENSMLUG00000006504	2 retrocopies	retro_mluc_2105, retro_mluc_385,
Macaca mulatta	ENSMMUG00000016806	1 retrocopy	retro_mmul_1092,
Mus musculus	ENSMUSG00000042670	2 retrocopies	retro_mmus_2571 , retro_mmus_591,
Nomascus leucogenys	ENSNLEG00000017882	1 retrocopy	retro_nleu_2484,
Oryctolagus cuniculus	ENSOCUG00000029612	1 retrocopy	retro_ocun_388,
Otolemur garnettii	ENSOGAG00000007853	3 retrocopies	retro_ogar_1202, retro_ogar_2006, retro_ogar_2643,
Pongo abelii	ENSPPYG00000003389	1 retrocopy	retro_pabe_747,
Pan troglodytes	ENSPTRG00000003472	1 retrocopy	retro_ptro_547,
Pteropus vampyrus	ENSPVAG00000015535	1 retrocopy	retro_pvam_932,
Rattus norvegicus	ENSRNOG00000004829	1 retrocopy	retro_rnor_2450,
Sarcophilus harrisii	ENSSHAG00000015407	2 retrocopies	retro_shar_396, retro_shar_491,
Sus scrofa	ENSSSCG00000013322	1 retrocopy	retro_sscr_1178,
Ictidomys tridecemlineatus	ENSSTOG00000003179	2 retrocopies	retro_itri_489, retro_itri_623,
Tupaia belangeri	ENSTBEG00000002126	6 retrocopies	retro_tbel_1510, retro_tbel_2503, retro_tbel_315, retro_tbel_3504, retro_tbel_4049, retro_tbel_878,
Tarsius syrichta	ENSTSYG00000009257	1 retrocopy	retro_tsyr_2139,
Tursiops truncatus	ENSTTRG00000002395	2 retrocopies	retro_ttru_1862, retro_ttru_966,
Vicugna pacos	ENSVPAG00000001940	1 retrocopy	retro_vpac_126,