RetrogeneDB ID: retro_mmus_576

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:79888711..79888882(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps21
• Ensembl ID: ENSMUSG00000039001
• Aliases: Rps21, 1810049N11Rik, 2410030A14Rik
• Description: ribosomal protein S21 [Source:MGI Symbol;Acc:MGI:1913731]

Sequence

>retro_mmus_576
ATGCAGAACGACGCCGGCGAGTTTGTGGACCTGTCCGTGCCTCGGAAATGCTCCGCATGCAACCTCATCATTGCTGCCAA
GGACCACGCGTCCATCCAGATGAACGTGGCCGAGGTTGATAGGACCACAGGCCGGTTTAATGGCCAGTTTAAAACTTACG
GCATCTGCGGG

Alignment

ORF - retro_mmus_576 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 68.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQNDAGEFVDLYVPRKCSASNRIIAAKDHASIQMNVAEVDRTTGRFNGQFKTYGICG
          MQNDAGEFVDL.VPRKCSA.N.IIAAKDHASIQMNVAEVDRTTGRFNGQFKTYGICG
Retrocopy MQNDAGEFVDLSVPRKCSACNLIIAAKDHASIQMNVAEVDRTTGRFNGQFKTYGICG

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	0.12 RPM	91.23 RPM
SRP007412_cerebellum	0.17 RPM	56.40 RPM
SRP007412_heart	0.09 RPM	82.68 RPM
SRP007412_kidney	0.19 RPM	73.67 RPM
SRP007412_liver	0.03 RPM	64.53 RPM
SRP007412_testis	0.00 RPM	35.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_576 was not detected

EST

No EST(s) were mapped for retro_mmus_576 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_5806	24 libraries	8 libraries	186 libraries	284 libraries	570 libraries

The graphical summary, for retro_mmus_576 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_576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_576 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017399	2 retrocopies	retro_amel_1783, retro_amel_87,
Bos taurus	ENSBTAG00000020795	2 retrocopies	retro_btau_174, retro_btau_1780,
Canis familiaris	ENSCAFG00000012676	4 retrocopies	retro_cfam_1055, retro_cfam_1687, retro_cfam_1896, retro_cfam_28,
Callithrix jacchus	ENSCJAG00000014195	5 retrocopies	retro_cjac_2266, retro_cjac_2572, retro_cjac_629, retro_cjac_82, retro_cjac_884,
Homo sapiens	ENSG00000171858	6 retrocopies	retro_hsap_1179, retro_hsap_1883, retro_hsap_2300, retro_hsap_2949, retro_hsap_3026, retro_hsap_4303,
Gorilla gorilla	ENSGGOG00000023745	7 retrocopies	retro_ggor_131, retro_ggor_1380, retro_ggor_1647, retro_ggor_2043, retro_ggor_2089, retro_ggor_2875, retro_ggor_917,
Latimeria chalumnae	ENSLACG00000012753	1 retrocopy	retro_lcha_124,
Monodelphis domestica	ENSMODG00000016769	1 retrocopy	retro_mdom_464,
Mus musculus	ENSMUSG00000039001	11 retrocopies	retro_mmus_1100, retro_mmus_1324, retro_mmus_1482, retro_mmus_1510, retro_mmus_1688, retro_mmus_1837, retro_mmus_2039, retro_mmus_2071, retro_mmus_2243, retro_mmus_576 , retro_mmus_992,
Ornithorhynchus anatinus	ENSOANG00000003361	2 retrocopies	retro_oana_102, retro_oana_107,
Otolemur garnettii	ENSOGAG00000016673	12 retrocopies	retro_ogar_1013, retro_ogar_1339, retro_ogar_1742, retro_ogar_2111, retro_ogar_2176, retro_ogar_2532, retro_ogar_2703, retro_ogar_2921, retro_ogar_3119, retro_ogar_3214, retro_ogar_3256, retro_ogar_719,
Pongo abelii	ENSPPYG00000011205	8 retrocopies	retro_pabe_1562, retro_pabe_157, retro_pabe_2446, retro_pabe_2505, retro_pabe_3503, retro_pabe_365, retro_pabe_710, retro_pabe_986,
Pan troglodytes	ENSPTRG00000013708	1 retrocopy	retro_ptro_42,
Rattus norvegicus	ENSRNOG00000006325	2 retrocopies	retro_rnor_128, retro_rnor_172,
Sus scrofa	ENSSSCG00000021825	1 retrocopy	retro_sscr_7,
Ictidomys tridecemlineatus	ENSSTOG00000001029	5 retrocopies	retro_itri_1027, retro_itri_1487, retro_itri_637, retro_itri_82, retro_itri_849,