RetrogeneDB ID: retro_mmus_3163

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:121581764..121582188(+)
• Located in intron of: ENSMUSG00000092329

Retrocopy information

• Ensembl ID: ENSMUSG00000097987
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rps23
• Ensembl ID: ENSMUSG00000049517
• Aliases: None
• Description: ribosomal protein S23 [Source:MGI Symbol;Acc:MGI:1913725]

Sequence

>retro_mmus_3163
ATGGGCAAGTGTCTTGGTCTCTGAACTGCCTGGAAGCTCGCAGTCACCGACGGGACCAGAAGTGGCATGATAAACAATAC
AAGAAAGCCCACTTGGGCACAGCCCTGAAGGCCAATCCGTTTGGGGTGCCTCTCATGCAAAGGGAATTGTGCTGGAAAAA
GTAGGGGTTGAGGCCAAACAGCCAAACTCTGCCATCAGGAAGTGTGTCAGGGTGCAGCTCATTAAGAATGGCAAGAAGAT
CACAGCGTTCGTGCCCAATGATGGCTGCCTGAACTTCATTGAGGAAAATGAAGTTCTAGTTGCTGGATTTGGTTGAAAAG
ATCATGCTGTAGATGATATTCCTGGAGTCCGCTTTAAGGTGGTTAAAGTAGCCAATGTTTCTCTGTTGGCTCTATACAAA
GGCAAGAAAGAAAGGCCAAGATCA

Alignment

ORF - retro_mmus_3163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKCRGLRTARKL-RSHRRDQKWHDKQYKKAHLGTALKANPFG-GASHAKGIVLEKVGVEAKQPNSAIRK
          MGKC.GL.TA.KL.RSHRRDQKWHDKQYKKAHLGTALKANPFG.GASHAKGIVLEKVGVEAKQPNSAIRK
Retrocopy MGKCLGL*TAWKL<RSHRRDQKWHDKQYKKAHLGTALKANPFG<GASHAKGIVLEKVGVEAKQPNSAIRK

Parental  CVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKK
          CVRVQLIKNGKKITAFVPNDGCLNFIEEN.EVLVAGFG.K.HAV.DIPGVRFKVVKVANVSLLALYKGKK
Retrocopy CVRVQLIKNGKKITAFVPNDGCLNFIEEN-EVLVAGFG*KDHAVDDIPGVRFKVVKVANVSLLALYKGKK

Parental  ERPRS
          ERPRS
Retrocopy ERPRS

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	40.46 RPM
SRP007412_cerebellum	0.00 RPM	22.32 RPM
SRP007412_heart	0.00 RPM	60.70 RPM
SRP007412_kidney	0.02 RPM	58.10 RPM
SRP007412_liver	0.00 RPM	55.65 RPM
SRP007412_testis	0.00 RPM	38.47 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3163 was not detected

EST

No EST(s) were mapped for retro_mmus_3163 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_139837	112 libraries	154 libraries	636 libraries	148 libraries	22 libraries

The graphical summary, for retro_mmus_3163 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_3163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3163 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011136	1 retrocopy	retro_acar_85,
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Mus musculus	ENSMUSG00000049517	12 retrocopies	retro_mmus_2151, retro_mmus_2200, retro_mmus_2690, retro_mmus_2812, retro_mmus_3118, retro_mmus_3163 , retro_mmus_3168, retro_mmus_323, retro_mmus_3619, retro_mmus_365, retro_mmus_836, retro_mmus_848,
Pongo abelii	ENSPPYG00000015608	7 retrocopies	retro_pabe_1538, retro_pabe_1585, retro_pabe_19, retro_pabe_2515, retro_pabe_2567, retro_pabe_2716, retro_pabe_3129,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Tursiops truncatus	ENSTTRG00000014491	6 retrocopies	retro_ttru_1253, retro_ttru_1555, retro_ttru_186, retro_ttru_458, retro_ttru_487, retro_ttru_578,