RetrogeneDB ID: retro_mmus_2733

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:53045883..53046430(+)
• Located in intron of: ENSMUSG00000063568

Retrocopy information

• Ensembl ID: ENSMUSG00000080759
• 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_2733
ATGGAGTTGGGCGAACTGCTGTACAACAAGTCGGAGTACATCGAGACGGCATCTGGGAACAAAAAGTTAGTCGCTAGTCT
GTTTTGTGGGAAGGCAGAACATCTTTCTCAATGGCAAGACCATTATAATGAACGACTGTATCATCCGAGGAGAACTCGCA
AGTGTAAGAGTTGGATGTCACTGTGTTGTGAAAAGCCGTAGTGTCATAAGGCCACCATTCAAAAAAATTCAGCAAAGGTG
TTACCTTCTTTCCTCTGCATATTGGGGATCATGTCTTTATTGAGGAAGACTGTGTGGTCAACGCTGCCCAGATTGGTTCT
TATGTTCACGTTGGGAGGAACTGTGTGACTGGGTGCCGTTGTGTCTTGAAAGACTGCTGCAAAATTCTTGACAATACAGT
ATTACCTCCAGAAACTGTGTTCCCCCCATTCACTGCCTTCTCCGGCTGCCCAGGACTCTCTCCGGGGAGCTCCCAGAGCG
CACACAGGAGCTGAGGAGTGATCTCACCAAAAGCTACAGCCAGAAGCTTCTACCCCTAGCACAAGTC

Alignment

ORF - retro_mmus_2733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MELGELLYNKSEYIETASGNKVSRQSVLCGS-QNIVLNGKTIIMNDCIIRGDLANVRVGRHCVVKSRSVI
          MELGELLYNKSEYIETASGNK....S..CG..QNI.LNGKTIIMNDCIIRG.LA.VRVG.HCVVKSRSVI
Retrocopy MELGELLYNKSEYIETASGNKKLVASLFCGK>QNIFLNGKTIIMNDCIIRGELASVRVGCHCVVKSRSVI

Parental  RPPFKK-FSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRCVLKDCCKILDNTVLPPET
          RPPFKK.FSKGV.FFPLHIGDHVFIEEDCVVNAAQIGSYVHVG.NCV.G.RCVLKDCCKILDNTVLPPET
Retrocopy RPPFKK>FSKGVTFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGRNCVTGCRCVLKDCCKILDNTVLPPET

Parental  VVPPFTVFSGCPGL-FSGELPECTQELMIDVTKSYYQKFLPLTQV
          V.PPFT.FSGCPGL..SGELPE.TQEL..D.TKSY.QK.LPL.QV
Retrocopy VFPPFTAFSGCPGL<LSGELPERTQELRSDLTKSYSQKLLPLAQV

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	0.07 RPM	62.33 RPM
SRP007412_cerebellum	0.04 RPM	49.59 RPM
SRP007412_heart	0.00 RPM	21.57 RPM
SRP007412_kidney	0.02 RPM	38.98 RPM
SRP007412_liver	0.03 RPM	19.61 RPM
SRP007412_testis	0.14 RPM	24.56 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2733 was not detected

EST

No EST(s) were mapped for retro_mmus_2733 retrocopy.

TSS

No TSS is located nearby retro_mmus_2733 retrocopy 5' end.

Lab

retro_mmus_2733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2733 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,