RetrogeneDB ID: retro_mmus_2252

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:53692424..53692878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Rps14
• Ensembl ID: ENSMUSG00000024608
• Aliases: Rps14, 2600014J02Rik, AL023078
• Description: ribosomal protein S14 [Source:MGI Symbol;Acc:MGI:98107]

Sequence

>retro_mmus_2252
ATGGCACCACGCAAGGGGAAGAAGGAAAAGAAGGAAGAGCAGGTCATCAGCCTGGGACCTCAGGTGGCTGAGGGAGAGAA
TGTGTTTGGTGTCTGCCACATCTTTGCATCCTTCAATGACACCTTTGTCCATGTTACCGATCTTTCTGGCAAGGAAACCA
TCTGCCGAGTGACTGGTGGGATGAAGGTGAAGGCTGACCGAGATGAGTCCTCTCTGTATGCAGCCATGTTGGCTGCCCAG
GATGTGGCCCAGAGGTGCAAGAAGCTGGGCATCACCGCCCTGCACATCAAACTCCGGGCCACAGGAGGAAACAGGACCAA
GACCCCTGGACCTGGAGCCCAGTCAGCCCTCAGAGCTCTTCTTGCTCTGGGATGAAGATTGGGCGGATTGAGGATGTCAC
CCCATTCCCTCTGATAGCACTGGAAGAAAGGGGGGTCGTCGTGGTCGCCGTCTG

Alignment

ORF - retro_mmus_2252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPRKG-KEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDES
          MAPRKG.KEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDES
Retrocopy MAPRKGKKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDES

Parental  SPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRAL-ARSGMKIGRIEDVT-PIPS
          S.YAAMLAAQDVAQRCK.LGITALHIKLRATGGNRTKTPGPGAQSALRAL...SGMKIGRIEDVT.PIPS
Retrocopy SLYAAMLAAQDVAQRCKKLGITALHIKLRATGGNRTKTPGPGAQSALRAL<SCSGMKIGRIEDVT<PIPS

Parental  DSTRRKGGRRGRRL
          DST.RKGGRRGRRL
Retrocopy DSTGRKGGRRGRRL

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	0.28 RPM	116.70 RPM
SRP007412_cerebellum	0.09 RPM	116.33 RPM
SRP007412_heart	0.25 RPM	133.21 RPM
SRP007412_kidney	0.69 RPM	171.55 RPM
SRP007412_liver	0.25 RPM	111.72 RPM
SRP007412_testis	0.32 RPM	156.43 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2252 was not detected

EST

No EST(s) were mapped for retro_mmus_2252 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_95103	8 libraries	0 libraries	10 libraries	19 libraries	1035 libraries

The graphical summary, for retro_mmus_2252 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_2252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2252 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Cavia porcellus	ENSCPOG00000024408	2 retrocopies	retro_cpor_253, retro_cpor_284,
Erinaceus europaeus	ENSEEUG00000010462	3 retrocopies	retro_eeur_330, retro_eeur_423, retro_eeur_617,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Loxodonta africana	ENSLAFG00000031195	2 retrocopies	retro_lafr_235, retro_lafr_67,
Myotis lucifugus	ENSMLUG00000013279	4 retrocopies	retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Mus musculus	ENSMUSG00000024608	5 retrocopies	retro_mmus_1362, retro_mmus_1924, retro_mmus_2178, retro_mmus_2252 , retro_mmus_2380,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Rattus norvegicus	ENSRNOG00000018774	10 retrocopies	retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Tursiops truncatus	ENSTTRG00000013035	1 retrocopy	retro_ttru_566,