RetrogeneDB ID: retro_mmus_625

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:24567818..24568134(-)
• Located in intron of: ENSMUSG00000087400

Retrocopy information

• Ensembl ID: ENSMUSG00000081259
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dctn5
• Ensembl ID: ENSMUSG00000030868
• Aliases: Dctn5, 4930427E12Rik, C78178
• Description: dynactin 5 [Source:MGI Symbol;Acc:MGI:1891689]

Sequence

>retro_mmus_625
ATGGAGTTGGGAGAACTGCTGTGTAACAACTCCGAGTACATAGAGACAGTGTCTGGGAACAAAGTTAGTCTCCAGTCTGG
TTTGTGTGGAAGCCAGAACATTGTTCTCAATGGCAAGACCATTATAATGAATGACTGTATCATCCAAGGAGACCTGGCAA
ACGTAGGAGTTGGACGTCACTGTGTTGTGAAAAGCCGTAGTGTCGTAAGGCTGCTGTTCAAAACAATTCAGCAAAGGTGT
TGTATTCTTTCCCCTGCATATTGGGGATCGTGTCTTTATTGAGGAAGACTGTGTGGTCAAGGCTGCCCAGATTGGT

Alignment

ORF - retro_mmus_625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIIMNDCIIRGDLANVRVGRHCVVKSRSVIR
          MELGELL.N.SEYIET.SGNKVS.QS.LCGSQNIVLNGKTIIMNDCII.GDLANV.VGRHCVVKSRSV.R
Retrocopy MELGELLCNNSEYIETVSGNKVSLQSGLCGSQNIVLNGKTIIMNDCIIQGDLANVGVGRHCVVKSRSVVR

Parental  PPF-KKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIG
          ..F.K.FSKGV.FFPLHIGD.VFIEEDCVV.AAQIG
Retrocopy LLF>KQFSKGVVFFPLHIGDRVFIEEDCVVKAAQIG

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	62.33 RPM
SRP007412_cerebellum	0.00 RPM	49.59 RPM
SRP007412_heart	0.00 RPM	21.57 RPM
SRP007412_kidney	0.02 RPM	38.98 RPM
SRP007412_liver	0.00 RPM	19.61 RPM
SRP007412_testis	0.00 RPM	24.56 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_625 was not detected

EST

No EST(s) were mapped for retro_mmus_625 retrocopy.

TSS

No TSS is located nearby retro_mmus_625 retrocopy 5' end.

Lab

retro_mmus_625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_625 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006410	1 retrocopy	retro_btau_1203,
Callithrix jacchus	ENSCJAG00000020623	1 retrocopy	retro_cjac_1687,
Homo sapiens	ENSG00000166847	1 retrocopy	retro_hsap_260,
Gorilla gorilla	ENSGGOG00000012834	1 retrocopy	retro_ggor_309,
Microcebus murinus	ENSMICG00000007806	1 retrocopy	retro_mmur_1082,
Myotis lucifugus	ENSMLUG00000012148	1 retrocopy	retro_mluc_140,
Mus musculus	ENSMUSG00000030868	2 retrocopies	retro_mmus_2733, retro_mmus_625 ,
Nomascus leucogenys	ENSNLEG00000012015	1 retrocopy	retro_nleu_863,
Pongo abelii	ENSPPYG00000007194	2 retrocopies	retro_pabe_1729, retro_pabe_405,
Pan troglodytes	ENSPTRG00000007891	1 retrocopy	retro_ptro_220,
Rattus norvegicus	ENSRNOG00000018048	2 retrocopies	retro_rnor_1351, retro_rnor_1847,