RetrogeneDB ID: retro_mmus_94

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:97098778..97099237(-)
• Located in intron of: ENSMUSG00000041817

Retrocopy information

• Ensembl ID: ENSMUSG00000057762
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Plp2
• Ensembl ID: ENSMUSG00000031146
• Aliases: None
• Description: proteolipid protein 2 [Source:MGI Symbol;Acc:MGI:1298382]

Sequence

>retro_mmus_94
ATGGCGGATTCTGAGCGTCTCTCGGCCCCCGGCTGCTGGTTAGCTTGCACCAGCTTCTCGCGCACCAAAAAGGGAATTCT
CCTGTTTGCTGAGATTATACTGTGCCTGGTGATTTTGATTTGCTTCAGTGCATCTACAACATCGGCCTACTCCTCCCTGT
CGGTGATTGAGATGATCTGTGCTGCTGTCTTACTTGTCTTCTACACGTGTGACCTGCACTCCAAGATATCATTCATCAAC
TGGCCTTGGACTGACTTCTTCAGATCCCTCATAGCAACCATCCTGTACCTGATCACCTCCATTGTTGTCCTTGTAGAAGG
AAGAGGCAGCTCCAGAGTTGTCGCTGGGATACTGGGCTTACTTGCTACGTTGCTCTTTGGCTACGATGCATACATCACCT
TCCCTCTAAAGCAGCAAAGACATACAGCAGCCCCCACTGACCCCACTGATGGCCCATGA

Alignment

ORF - retro_mmus_94 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  MADSERLSAPGCWLACTSFSRTKKGILLFAEIILCLVILICFSASTTSAYSSLSVIEMICAAVLLVFYTC
          MADSERLSAPGCWLACTSFSRTKKGILLFAEIILCLVILICFSASTTSAYSSLSVIEMICAAVLLVFYTC
Retrocopy MADSERLSAPGCWLACTSFSRTKKGILLFAEIILCLVILICFSASTTSAYSSLSVIEMICAAVLLVFYTC

Parental  DLHSKISFINWPWTDFFRSLIATILYLITSIVVLVEGRGSSRVVAGILGLLATLLFGYDAYITFPLKQQR
          DLHSKISFINWPWTDFFRSLIATILYLITSIVVLVEGRGSSRVVAGILGLLATLLFGYDAYITFPLKQQR
Retrocopy DLHSKISFINWPWTDFFRSLIATILYLITSIVVLVEGRGSSRVVAGILGLLATLLFGYDAYITFPLKQQR

Parental  HTAAPTDPTDGP
          HTAAPTDPTDGP
Retrocopy HTAAPTDPTDGP

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	2.06 RPM
SRP007412_cerebellum	0.00 RPM	1.17 RPM
SRP007412_heart	0.03 RPM	12.67 RPM
SRP007412_kidney	0.04 RPM	8.30 RPM
SRP007412_liver	0.00 RPM	0.57 RPM
SRP007412_testis	0.00 RPM	0.91 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_94 was not detected

EST

No EST(s) were mapped for retro_mmus_94 retrocopy.

TSS

No TSS is located nearby retro_mmus_94 retrocopy 5' end.

Lab

retro_mmus_94 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_94 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012288	1 retrocopy	retro_amel_1129,
Bos taurus	ENSBTAG00000016093	3 retrocopies	retro_btau_1574, retro_btau_73, retro_btau_810,
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933,
Equus caballus	ENSECAG00000000216	1 retrocopy	retro_ecab_971,
Felis catus	ENSFCAG00000003820	2 retrocopies	retro_fcat_1547, retro_fcat_256,
Homo sapiens	ENSG00000102007	1 retrocopy	retro_hsap_3411,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427,
Macaca mulatta	ENSMMUG00000023022	1 retrocopy	retro_mmul_2124,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94 ,
Nomascus leucogenys	ENSNLEG00000001317	1 retrocopy	retro_nleu_2887,
Otolemur garnettii	ENSOGAG00000003865	3 retrocopies	retro_ogar_2568, retro_ogar_2865, retro_ogar_473,
Pan troglodytes	ENSPTRG00000021885	1 retrocopy	retro_ptro_2316,
Pteropus vampyrus	ENSPVAG00000011770	2 retrocopies	retro_pvam_1214, retro_pvam_810,
Rattus norvegicus	ENSRNOG00000039496	1 retrocopy	retro_rnor_2686,
Tursiops truncatus	ENSTTRG00000016968	2 retrocopies	retro_ttru_1586, retro_ttru_767,