RetrogeneDB ID: retro_mmus_2014

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:20235047..20236097(-)
• Located in intron of: ENSMUSG00000036617

Retrocopy information

• Ensembl ID: ENSMUSG00000081128
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrps5
• Ensembl ID: ENSMUSG00000027374
• Aliases: None
• Description: mitochondrial ribosomal protein S5 [Source:MGI Symbol;Acc:MGI:1924971]

Sequence

>retro_mmus_2014
CAGAATTTAAGACAGCAAACCTGTTTCATTGCAGTGACTGCAGAAGAGCTCTGGAAAGGCGCCTTAGCAGAGACTGGAGC
TGGAGCAAGAAAAGGCAGAGGCAAAAGAACAAAGAAAAAGAAGAGGAAGGATTTGAACAGGGGCCAGATTATTGGTGAAA
GGCGCTCTGGCTTCCTGTGGCCCGGTTTGAATGTTCCTCTGATAAAAAGTGGGGTCGTCCAGAACATCGGCCAGAGAAGC
AAAGAGGAGCAGCAGAAGGTGGAGGCCACCATGGTCGAGCAGCGAGAGGAGTGGGACCGGAAGAGGAAGATCAAAGTTAA
ACGGGAGCGCGGCTGGAGTGGGAACACGTGGGGGGGGGTGTCAGTATTGGCCCCCCAGACCCGGGACCCAATGGAGAAAC
ATATGAAGACTTTGATACCAGGATTCTTGATGTAAGAAATGTCTTCAATATGACAGCAAAAGAGGGAAGAAAGAAGTCGG
TCCGAGTCCTGGTTGCTGTTGGGAATGGAAATGGAGCTGCAGGTTTTGCTATTGGGAAAGCCGCTGACCGGGCAGGCGCT
TTCAGAAAGGCAAAGAACCGAGAGATTCATTATTTGCATTACATAGAACACATACGAAGGACATACAATATTCCATGACA
TTTCCCTAAGATTCAAAAGGACACAGATCCGGATGAAGAAACAACCCAGAGGTTACGGCCTCCGCTGCCACAGGGCCATT
ATCAACATCTGCCGCCTCATCGGCATCAAGGACATGTATGCGAGGGTCACCGGGTCCATGAACATGCTCAACCTCACCCG
GGGCCTCTTCCATGGGCTTGCCCGCCAGGAAACCCACCAACATCTGGCGGATAAGAAGGGTCTCCACGTGGTGGAATTCC
GGGAGGAATGTGGGCCTCTGCCTATCGTGGTGGCCTCCCCACATGGGGCCTTGAGTAAGGAGCCGGAGCCGGAACCTGAG
GTTCCTGATACCAAGCTGGACTGGCAGGACGTGAAGGCCATGCAGGGACTGAAGCGCTCTGTGTGGTTTAATTTAAAGAG
GCCTGCCACC

Alignment

ORF - retro_mmus_2014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.9 %
• Parental protein coverage: 80.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QQCRPYSFFTKLTAEELWKGALAETGAGARKGRGKRTKKKKRKDLNRGQIIGEGRSGFLWPGLNVPLIKS
          Q..R....F...TAEELWKGALAETGAGARKGRGKRTKKKKRKDLNRGQIIGE.RSGFLWPGLNVPLIKS
Retrocopy QNLRQQTCFIAVTAEELWKGALAETGAGARKGRGKRTKKKKRKDLNRGQIIGERRSGFLWPGLNVPLIKS

Parental  GVVQNIGQRSKEEQQKVEATMVEQREEWDRKRKIKVKRERGWSGNTWGGVSI-GPP-DPGPNGETYEDFD
          GVVQNIGQRSKEEQQKVEATMVEQREEWDRKRKIKVKRERGWSGNT....S...PP.DPGPNGETYEDFD
Retrocopy GVVQNIGQRSKEEQQKVEATMVEQREEWDRKRKIKVKRERGWSGNTXXXXSV>WPP>DPGPNGETYEDFD

Parental  TRILEVRNVFNMTAKEGRKKSVRVLVAVGNGNGAAGFAIGKAADRGDAFRKAKNRAIHYLHYIER-YEGH
          TRIL.VRNVFNMTAKEGRKKSVRVLVAVGNGNGAAGFAIGKAADR..AFRKAKNR.IHYLHYIE..YEGH
Retrocopy TRILDVRNVFNMTAKEGRKKSVRVLVAVGNGNGAAGFAIGKAADRAGAFRKAKNREIHYLHYIEH>YEGH

Parental  TIFHDISLRFKRTQIRMKKQPRGYGLRCHRAIITICRLIGIKDMYARVTGSMNMLNLTRGLFHGLARQET
          TIFHDISLRFKRTQIRMKKQPRGYGLRCHRAII.ICRLIGIKDMYARVTGSMNMLNLTRGLFHGLARQET
Retrocopy TIFHDISLRFKRTQIRMKKQPRGYGLRCHRAIINICRLIGIKDMYARVTGSMNMLNLTRGLFHGLARQET

Parental  HQHLADKKGLHVVEFREECGPLPIVVASPHGALSKEPEPEPEVPDTKLDWQDVKAMQGLKRSVWFNLKRP
          HQHLADKKGLHVVEFREECGPLPIVVASPHGALSKEPEPEPEVPDTKLDWQDVKAMQGLKRSVWFNLKRP
Retrocopy HQHLADKKGLHVVEFREECGPLPIVVASPHGALSKEPEPEPEVPDTKLDWQDVKAMQGLKRSVWFNLKRP

Parental  AT
          AT
Retrocopy AT

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	0.09 RPM	28.20 RPM
SRP007412_cerebellum	0.00 RPM	41.73 RPM
SRP007412_heart	0.09 RPM	24.53 RPM
SRP007412_kidney	0.19 RPM	31.09 RPM
SRP007412_liver	0.08 RPM	28.62 RPM
SRP007412_testis	0.00 RPM	16.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2014 was not detected

EST

No EST(s) were mapped for retro_mmus_2014 retrocopy.

TSS

No TSS is located nearby retro_mmus_2014 retrocopy 5' end.

Lab

retro_mmus_2014 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2014 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009757	1 retrocopy	retro_amel_1242,
Callithrix jacchus	ENSCJAG00000018942	1 retrocopy	retro_cjac_2129,
Homo sapiens	ENSG00000144029	1 retrocopy	retro_hsap_3116,
Gorilla gorilla	ENSGGOG00000001750	1 retrocopy	retro_ggor_2139,
Microcebus murinus	ENSMICG00000007318	1 retrocopy	retro_mmur_565,
Myotis lucifugus	ENSMLUG00000003183	1 retrocopy	retro_mluc_2245,
Macaca mulatta	ENSMMUG00000016239	2 retrocopies	retro_mmul_2110, retro_mmul_2251,
Mus musculus	ENSMUSG00000027374	1 retrocopy	retro_mmus_2014 ,
Nomascus leucogenys	ENSNLEG00000000002	1 retrocopy	retro_nleu_1438,
Pongo abelii	ENSPPYG00000012051	1 retrocopy	retro_pabe_2574,
Pan troglodytes	ENSPTRG00000012209	1 retrocopy	retro_ptro_2107,