RetrogeneDB ID: retro_mmus_2374

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:88043803..88044035(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081530
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lyrm4
• Ensembl ID: ENSMUSG00000046573
• Aliases: Lyrm4, BC034664, Gm903
• Description: LYR motif containing 4 [Source:MGI Symbol;Acc:MGI:2683538]

Sequence

>retro_mmus_2374
TACTGGGCAATGCCGAGGGAGAACAGAGTTTGAGTGCCCATGATAACAGAATACATGCTGTCATGAAGGTAGAAGATGCC
TTCTGAGAAAATAAAAATGTAAAAGCTCCAGTAGAAATTCAAATCCTAGTGAATAAAGCCAAAGAGACCTTGAAATTATC
CATCCACTGGCCCATACTGTCTACCTGTATTGGACTGACAAGCTTATCCCTGATGATCAAGAGAAGCAGAGG

Alignment

ORF - retro_mmus_2374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YRAMMRESK-HFSAYNYRMYAVRRIRDAFRENKNVKDPVEIQALVNKAK-RDLEIIRRQVHIGQLYSTDK
          Y.AM.RE.....SA...R..AV....DAF.ENKNVK.PVEIQ.LVNKAK.RDLEII....H...LY.TDK
Retrocopy YWAMPRENR<SLSAHDNRIHAVMKVEDAF*ENKNVKAPVEIQILVNKAK<RDLEIIHPLAHTVYLYWTDK

Parental  LIIENQEKPR
          LI...QEK.R
Retrocopy LIPDDQEKQR

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	15.98 RPM
SRP007412_cerebellum	0.00 RPM	9.77 RPM
SRP007412_heart	0.00 RPM	8.72 RPM
SRP007412_kidney	0.00 RPM	12.30 RPM
SRP007412_liver	0.00 RPM	5.95 RPM
SRP007412_testis	0.00 RPM	5.17 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2374 was not detected

EST

No EST(s) were mapped for retro_mmus_2374 retrocopy.

TSS

No TSS is located nearby retro_mmus_2374 retrocopy 5' end.

Lab

retro_mmus_2374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2374 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031432	1 retrocopy	retro_btau_783,
Callithrix jacchus	ENSCJAG00000021370	1 retrocopy	retro_cjac_1371,
Homo sapiens	ENSG00000214113	1 retrocopy	retro_hsap_194,
Macropus eugenii	ENSMEUG00000005958	1 retrocopy	retro_meug_656,
Myotis lucifugus	ENSMLUG00000028065	1 retrocopy	retro_mluc_394,
Mustela putorius furo	ENSMPUG00000000532	1 retrocopy	retro_mputfur_1459,
Mus musculus	ENSMUSG00000046573	1 retrocopy	retro_mmus_2374 ,
Nomascus leucogenys	ENSNLEG00000011472	1 retrocopy	retro_nleu_1002,
Rattus norvegicus	ENSRNOG00000047970	2 retrocopies	retro_rnor_1862, retro_rnor_2052,
Tursiops truncatus	ENSTTRG00000007073	1 retrocopy	retro_ttru_552,