RetrogeneDB ID: retro_mmus_1696

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:15011245..15011689(+)
• Located in intron of: ENSMUSG00000036225

Retrocopy information

• Ensembl ID: ENSMUSG00000071867
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl27
• Ensembl ID: ENSMUSG00000024414
• Aliases: Mrpl27, A630055F16Rik, D11Moh47, D18Ertd643e
• Description: mitochondrial ribosomal protein L27 [Source:MGI Symbol;Acc:MGI:2137224]

Sequence

>retro_mmus_1696
ATGGCGGCGGCGGCGCTTACGCTGAGGACGCGGGCAGCAGTGACAGCCCTGCTGAGCCCCACAGCACCCACAGCACTCGC
TGTCAGACATGCATCCAAGAAGACAGGTGGCAGCTCTAAGAACCTTGGTGGGAAATCACGAGGCAAACACTACGGCATCA
AGAAAATGGAAGGTCACTACGTTCACGCTGGCAACATCCTTGGCACTCAGCGTCAGTTTAGATGGCACCCAGGAGCCCAT
GTGGGACTTGGGAGGAACAAGTGCCTGTATGCCCTGGAGGAGGGGATAGTCCGCTACACGAAAGACGTCTACGTGCCCAA
TCCCAAAAACACAGAGGCTGTGGATCTGGTCACTAGTCTGCCCAAGGGTGCTGTGCTCTACAAGACTTTTGTCCACGTAG
TTCCTGCCAAACCTGAGGGAACCTTCAAACTAGTGGACATGCTT

Alignment

ORF - retro_mmus_1696 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  MAAAALTLRTRAAVTALLSPTAPTALAVRHASKKTGGSSKNLGGKSRGKHYGIKKMEGHYVHAGNILGTQ
          MAAAALTLRTRAAVTALLSPTAPTALAVRHASKKTGGSSKNLGGKSRGKHYGIKKMEGHYVHAGNILGTQ
Retrocopy MAAAALTLRTRAAVTALLSPTAPTALAVRHASKKTGGSSKNLGGKSRGKHYGIKKMEGHYVHAGNILGTQ

Parental  RQFRWHPGAHVGLGRNKCLYALEEGIVRYTKDVYVPNPKNTEAVDLVTSLPKGAVLYKTFVHVVPAKPEG
          RQFRWHPGAHVGLGRNKCLYALEEGIVRYTKDVYVPNPKNTEAVDLVTSLPKGAVLYKTFVHVVPAKPEG
Retrocopy RQFRWHPGAHVGLGRNKCLYALEEGIVRYTKDVYVPNPKNTEAVDLVTSLPKGAVLYKTFVHVVPAKPEG

Parental  TFKLVDML
          TFKLVDML
Retrocopy TFKLVDML

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	0.02 RPM	16.28 RPM
SRP007412_cerebellum	0.00 RPM	10.90 RPM
SRP007412_heart	0.09 RPM	14.94 RPM
SRP007412_kidney	0.10 RPM	17.86 RPM
SRP007412_liver	0.14 RPM	20.51 RPM
SRP007412_testis	0.00 RPM	3.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1696 was not detected

EST

2 EST(s) were mapped to retro_mmus_1696 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BY084396	15011239	15011456	98.2	213	4	209
CD297650	15011224	15011401	100	177	0	177

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_57945	537 libraries	445 libraries	87 libraries	2 libraries	1 library

The graphical summary, for retro_mmus_1696 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_1696 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1696 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017031	1 retrocopy	retro_cfam_1454,
Choloepus hoffmanni	ENSCHOG00000005103	1 retrocopy	retro_chof_943,
Callithrix jacchus	ENSCJAG00000018851	2 retrocopies	retro_cjac_28, retro_cjac_378,
Dasypus novemcinctus	ENSDNOG00000023845	2 retrocopies	retro_dnov_1233, retro_dnov_1731,
Erinaceus europaeus	ENSEEUG00000010549	3 retrocopies	retro_eeur_126, retro_eeur_22, retro_eeur_9,
Echinops telfairi	ENSETEG00000014252	2 retrocopies	retro_etel_13, retro_etel_893,
Microcebus murinus	ENSMICG00000009698	1 retrocopy	retro_mmur_624,
Macaca mulatta	ENSMMUG00000017231	1 retrocopy	retro_mmul_64,
Mus musculus	ENSMUSG00000024414	2 retrocopies	retro_mmus_1696 , retro_mmus_2918,
Oryctolagus cuniculus	ENSOCUG00000004601	2 retrocopies	retro_ocun_1026, retro_ocun_1936,
Otolemur garnettii	ENSOGAG00000005385	1 retrocopy	retro_ogar_53,