RetrogeneDB ID: retro_mmus_3174

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:11714814..11715239(-)
• Located in intron of: ENSMUSG00000031510

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl26
• Ensembl ID: ENSMUSG00000060938
• Aliases: Rpl26, SIG-20
• Description: ribosomal protein L26 [Source:MGI Symbol;Acc:MGI:106022]

Sequence

>retro_mmus_3174
ATGAAGTTCAATCCCTTCGTGACTTCTGACCGAAGCAAAGAACTGCAAGCGGCATGTCAATGCGCCCTCTCACATTCGGA
GGAAGATCACGTCTTCCCCTCTTTCCAGAGCTGAGACAGAAGTATAACTTTCGGTCTATGCCCATTCGGAAGGATGATGA
AGTTCAGTTTGTTCAAGGACACTACAAAGGCCAGCAGATTGGCAAGGTGGTCCAGGTGTACAGGAAGAAATATGTCATCT
ACATCGAACGCGTCCAGCGAGAGAAGGCTAATAGCACAACCGTCCACGTGGGCATCCACCCCAGCAAGGTCGTTATCACC
AGGCTAAAGCTGGACAAGGACTGCAAGAAGATCCTGGAGAGGAAAGCCGAGTCCCGACAAGTAGGAAAGGAGAAGGGCAA
ATACAAGGAAGAAACGATCGATCGA

Alignment

ORF - retro_mmus_3174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 97.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSK-NRKRHFNAPSHIRRKIMSS-PLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIG
          MKFNPFVTSDRSK.N.KRH.NAPSHI.R....S.PL..ELRQKYN.RSMPIRKDDEVQ.V.GHYKGQQIG
Retrocopy MKFNPFVTSDRSK>NCKRHVNAPSHI-RRKITS>PLFPELRQKYNFRSMPIRKDDEVQFVQGHYKGQQIG

Parental  KVVQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEE
          KVVQVYRKKYVIYIERVQREKAN.TTVHVGIHPSKVVITRLKLDKD.KKILERKA.SRQVGKEKGKYKEE
Retrocopy KVVQVYRKKYVIYIERVQREKANSTTVHVGIHPSKVVITRLKLDKDCKKILERKAESRQVGKEKGKYKEE

Parental  TIEK
          TI..
Retrocopy TIDR

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	82.07 RPM
SRP007412_cerebellum	0.04 RPM	43.77 RPM
SRP007412_heart	0.03 RPM	61.58 RPM
SRP007412_kidney	0.06 RPM	56.40 RPM
SRP007412_liver	0.11 RPM	60.43 RPM
SRP007412_testis	0.09 RPM	61.02 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3174 was not detected

EST

No EST(s) were mapped for retro_mmus_3174 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_139291	191 libraries	443 libraries	414 libraries	19 libraries	5 libraries

The graphical summary, for retro_mmus_3174 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_3174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3174 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Gorilla gorilla	ENSGGOG00000023944	4 retrocopies	retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Mus musculus	ENSMUSG00000060938	21 retrocopies	retro_mmus_1325, retro_mmus_1444, retro_mmus_1506, retro_mmus_1642, retro_mmus_1866, retro_mmus_1978, retro_mmus_2011, retro_mmus_2218, retro_mmus_2435, retro_mmus_2540, retro_mmus_2673, retro_mmus_3078, retro_mmus_3174 , retro_mmus_320, retro_mmus_3270, retro_mmus_3291, retro_mmus_3361, retro_mmus_384, retro_mmus_556, retro_mmus_900, retro_mmus_939,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Oryctolagus cuniculus	ENSOCUG00000006538	11 retrocopies	retro_ocun_1125, retro_ocun_1290, retro_ocun_1442, retro_ocun_1484, retro_ocun_1515, retro_ocun_1621, retro_ocun_1917, retro_ocun_529, retro_ocun_542, retro_ocun_589, retro_ocun_803,
Pan troglodytes	ENSPTRG00000008742	3 retrocopies	retro_ptro_1546, retro_ptro_2510, retro_ptro_73,
Rattus norvegicus	ENSRNOG00000004214	3 retrocopies	retro_rnor_213, retro_rnor_260, retro_rnor_273,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,