RetrogeneDB ID: retro_mmus_2949

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:83799468..83799657(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps28
• Ensembl ID: ENSMUSG00000067288
• Aliases: None
• Description: ribosomal protein S28 [Source:MGI Symbol;Acc:MGI:1859516]

Sequence

>retro_mmus_2949
ATGAACACTGTTGTACTGCAACCCATTAGGCTAACCTGGGTCACCACAGTGCTGTGCAGGACCAGCTCCCAGGCACAGTG
CCTACAGGTGTGCATGGAACATACGGTCAGCACCAGCTACTCCATCACATCCAAGGTGAAAGATGCAGTGCACGAGAGTG
ATGTGCCCACCTTGCTGGAGTCAGAACGG

Alignment

ORF - retro_mmus_2949 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 91.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESER
          M.T...QPI.L..VT.VL.RT.SQ.QC.QV..E....TS.SI...VK..V.E.DV.TLLESER
Retrocopy MNTVVLQPIRLTWVTTVLCRTSSQAQCLQVCMEHTVSTSYSITSKVKDAVHESDVPTLLESER

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	22.83 RPM
SRP007412_cerebellum	0.00 RPM	15.76 RPM
SRP007412_heart	0.00 RPM	36.02 RPM
SRP007412_kidney	0.00 RPM	40.14 RPM
SRP007412_liver	0.00 RPM	35.45 RPM
SRP007412_testis	0.00 RPM	44.73 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2949 was not detected

EST

No EST(s) were mapped for retro_mmus_2949 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_137756	1058 libraries	3 libraries	6 libraries	4 libraries	1 library

The graphical summary, for retro_mmus_2949 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_2949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2949 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004917	1 retrocopy	retro_amel_1359,
Bos taurus	ENSBTAG00000002468	1 retrocopy	retro_btau_1130,
Cavia porcellus	ENSCPOG00000022876	5 retrocopies	retro_cpor_1092, retro_cpor_1485, retro_cpor_1504, retro_cpor_176, retro_cpor_702,
Equus caballus	ENSECAG00000017256	1 retrocopy	retro_ecab_725,
Felis catus	ENSFCAG00000024931	3 retrocopies	retro_fcat_1130, retro_fcat_611, retro_fcat_752,
Homo sapiens	ENSG00000233927	9 retrocopies	retro_hsap_1192, retro_hsap_1352, retro_hsap_1725, retro_hsap_2220, retro_hsap_2279, retro_hsap_3748, retro_hsap_505, retro_hsap_523, retro_hsap_799,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Myotis lucifugus	ENSMLUG00000023621	1 retrocopy	retro_mluc_2040,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122, retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949 , retro_mmus_3283, retro_mmus_91,
Oryctolagus cuniculus	ENSOCUG00000021484	2 retrocopies	retro_ocun_1230, retro_ocun_1799,
Pan troglodytes	ENSPTRG00000040141	6 retrocopies	retro_ptro_1228, retro_ptro_1613, retro_ptro_3037, retro_ptro_378, retro_ptro_391, retro_ptro_927,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95, retro_rnor_96,
Sus scrofa	ENSSSCG00000013597	3 retrocopies	retro_sscr_132, retro_sscr_191, retro_sscr_808,