RetrogeneDB ID: retro_mmus_71

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:50344296..50344941(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000058443
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rpl10
• Ensembl ID: ENSMUSG00000008682
• Aliases: Rpl10, D0HXS648, DXHXS648, DXHXS648E, QM, QM16
• Description: ribosomal protein L10 [Source:MGI Symbol;Acc:MGI:105943]

Sequence

>retro_mmus_71
ATGGGCCGCCGCCCCGCCCGGTGTTACCGGTATTGTAAGAACAAGCCATACCCAAAGTCTCGTTTCTGCCGTGGTGTCCC
TGATGCTAAGATCCGAATCTTTGATTTGGGACGGAAGAAAGCAAAAGTTGATGAATTCCCACTTTGTGGCCATATGGTGT
CAGATGAATATGAGCAACTCTCTTCTGAAGCACTGGAGGCTGCCCGTATTTGTGCCAACAAATACATGGTAAAGAGTTGT
GGCAAGGATGGCTTTCATATCCGAGTGAGGCTCCACCCTTTCCATGTCATCCGTATCAACAAGATGTTGTCCTGTGCTGG
GGCTGACAGGCTCCAGACAGGGATGCGTGGTGCCTTTGGGAAGCCCCAGGGCACAGTGGCCAGGGTTCACATTGGCCAGG
TCATCATGTCCATCCGAACCAAGTTGCAGAACAAGGAACATGTGATTGAGGCTCTGCGAAGAGCCAAGTTCAAGTTCCCT
GGCCGCCAGAAGATCCACATCTCAAAGAAGTGGGGCTTCACCAAGTTTAATGCAGATGAATTTGAAGACATGGTTGCTGA
GAAGCGGCTCATTCCTGATGGCTGTGGTGTCAAATATATCCCCAATCGTGGTCCTCTGGACAAGTGGAGAGCCCTGCATT
CCTGA

Alignment

ORF - retro_mmus_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
          MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
Retrocopy MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
          CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
Retrocopy CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT

Parental  KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
          KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
Retrocopy KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR

Parental  ALHS
          ALHS
Retrocopy ALHS

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	51.05 RPM
SRP007412_cerebellum	0.04 RPM	22.01 RPM
SRP007412_heart	0.00 RPM	53.98 RPM
SRP007412_kidney	0.00 RPM	70.36 RPM
SRP007412_liver	0.05 RPM	96.48 RPM
SRP007412_testis	0.00 RPM	8.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_71 was not detected

EST

No EST(s) were mapped for retro_mmus_71 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_150858	49 libraries	26 libraries	577 libraries	326 libraries	94 libraries

The graphical summary, for retro_mmus_71 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_71 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_71 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007454	2 retrocopies	retro_btau_140, retro_btau_99,
Cavia porcellus	ENSCPOG00000002355	1 retrocopy	retro_cpor_64,
Equus caballus	ENSECAG00000017154	1 retrocopy	retro_ecab_113,
Homo sapiens	ENSG00000147403	3 retrocopies	retro_hsap_2030, retro_hsap_3265, retro_hsap_3437,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Microcebus murinus	ENSMICG00000004658	2 retrocopies	retro_mmur_1077, retro_mmur_4,
Myotis lucifugus	ENSMLUG00000014337	3 retrocopies	retro_mluc_1592, retro_mluc_191, retro_mluc_275,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Mustela putorius furo	ENSMPUG00000009320	3 retrocopies	retro_mputfur_1405, retro_mputfur_54, retro_mputfur_84,
Mus musculus	ENSMUSG00000008682	1 retrocopy	retro_mmus_71 ,
Otolemur garnettii	ENSOGAG00000000099	3 retrocopies	retro_ogar_293, retro_ogar_2995, retro_ogar_3284,
Pongo abelii	ENSPPYG00000020874	5 retrocopies	retro_pabe_173, retro_pabe_1854, retro_pabe_2036, retro_pabe_2843, retro_pabe_2955,
Ictidomys tridecemlineatus	ENSSTOG00000011857	2 retrocopies	retro_itri_174, retro_itri_506,