RetrogeneDB ID: retro_mmus_474

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:102458658..102458922(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lyrm2
• Ensembl ID: ENSMUSG00000045854
• Aliases: None
• Description: LYR motif containing 2 [Source:MGI Symbol;Acc:MGI:1917573]

Sequence

>retro_mmus_474
ATGGCTGCTTCCTGCTTGCCACCTGCGGCCCTGATGCTGAAGCAGTTCATGAGAAGGCAGCAACTTCTCCTCCTCTACAG
AAAGATTTTGCAAGCAATTAGGCAAGTTCCAAGTGATTCTGACTGAAAATACCTTCAGGATTGGGCCAGGGAAGAATTTA
AAAGAAACAAAAGTGCCACAGAAGAGAATACAATCCGAATGATAATTATCCAAGGCAATATGCAGCTAAAGGAACTAGAA
AGGATGCTTGCCTTAGCCAACTCG

Alignment

ORF - retro_mmus_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASRLPPAALTLKQFMRRQQVLLLYRKILRAIRQVPSDSDRKYLQDWAREEFKRNKSATEEDTIRMMIT
          MAAS.LPPAAL.LKQFMRRQQ.LLLYRKIL.AIRQVPSDSD.KYLQDWAREEFKRNKSATEE.TIRM.I.
Retrocopy MAASCLPPAALMLKQFMRRQQLLLLYRKILQAIRQVPSDSD*KYLQDWAREEFKRNKSATEENTIRMIII

Parental  QGNMQLKELERTLALANS
          QGNMQLKELER.LALANS
Retrocopy QGNMQLKELERMLALANS

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	8.32 RPM
SRP007412_cerebellum	0.00 RPM	5.78 RPM
SRP007412_heart	0.00 RPM	15.07 RPM
SRP007412_kidney	0.00 RPM	18.27 RPM
SRP007412_liver	0.00 RPM	7.13 RPM
SRP007412_testis	0.00 RPM	11.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_474 was not detected

EST

No EST(s) were mapped for retro_mmus_474 retrocopy.

TSS

No TSS is located nearby retro_mmus_474 retrocopy 5' end.

Lab

retro_mmus_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_474 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000009916	1 retrocopy	retro_meug_2134,
Microcebus murinus	ENSMICG00000012230	2 retrocopies	retro_mmur_631, retro_mmur_650,
Mus musculus	ENSMUSG00000045854	2 retrocopies	retro_mmus_474 , retro_mmus_790,
Otolemur garnettii	ENSOGAG00000034900	1 retrocopy	retro_ogar_508,
Sus scrofa	ENSSSCG00000004324	1 retrocopy	retro_sscr_686,
Ictidomys tridecemlineatus	ENSSTOG00000016198	1 retrocopy	retro_itri_1279,
Tursiops truncatus	ENSTTRG00000007420	1 retrocopy	retro_ttru_1516,