RetrogeneDB ID: retro_mmus_477

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:107138058..107138569(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083884
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rps6
• Ensembl ID: ENSMUSG00000028495
• Aliases: None
• Description: ribosomal protein S6 [Source:MGI Symbol;Acc:MGI:98159]

Sequence

>retro_mmus_477
ATGAAGCTGAATATCTCTTTCCCTGGCACTGGCTGTCAGAAGCTCATTGAAGTGGATGACCAACACAAGCTTCGCACATT
CTATGAGAAGTGCATGGCCACAGAAGTTGCTGCTGATGCTCTTGGTGAGGATTAGAAGGGTTATGTGGCTGGATCAGCCA
GCGGTGGGAATGAAAGGCAAGTTTTCCCATGAAGCAAGGCATTTTGACCCATAGCAGAGTAAACCTGTTGTTGAGTAAGA
GGCATTCCTGTTATAGACCAAGGAGAACTGGAGACAGAAAGTTCAAGTCTGTTTGAGGATGCATTGTGGACGGTAATCTC
AGTGTTCTCAATTTGTTATTGTAAAGAAAGGAAAGAAGCATATTCCAGGACTGACAGATACTACTGTGCCTCATCCATTG
GGACCTAAAAGAGCTAGTAGAATGTGAAAGCTTTTTAATCTCTCCAAAGATGACGTCTGCCAGTATGTTGTCAGGAAGCC
CTAAAACAAAGATTGTAAGAAGCCCAGGACC

Alignment

ORF - retro_mmus_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 68.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVV-RISGGNDKQ-GFPMKQGVL
          MKLNISFP.TGCQKLIEVDD..KLRTFYEK.MATEVAADALGE..KGYV....SGGN..Q..FPMKQG.L
Retrocopy MKLNISFPGTGCQKLIEVDDQHKLRTFYEKCMATEVAADALGED*KGYVAGSASGGNERQ<SFPMKQGIL

Parental  THGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNL-VIVKKGEKDIPGLTDTTVPRRLGPKR
          TH.RV.LLLSK.HSCYRPRRTG.RK.KSV.GCIVD.NLSVLNL.VIVKKG.K.IPGLTDTTVP..LGPKR
Retrocopy THSRVNLLLSKRHSCYRPRRTGDRKFKSV*GCIVDGNLSVLNL<VIVKKGKKHIPGLTDTTVPHPLGPKR

Parental  ASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRT
          ASR..KLFNLSK.DDV.QYVVRKP.NK..KKPRT
Retrocopy ASRM*KLFNLSK-DDVCQYVVRKP*NKDCKKPRT

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	43.48 RPM
SRP007412_cerebellum	0.00 RPM	37.30 RPM
SRP007412_heart	0.00 RPM	69.30 RPM
SRP007412_kidney	0.00 RPM	72.19 RPM
SRP007412_liver	0.00 RPM	80.59 RPM
SRP007412_testis	0.00 RPM	43.50 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_477 was not detected

EST

No EST(s) were mapped for retro_mmus_477 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_68127	689 libraries	360 libraries	23 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_477 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_477 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_477 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 135 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Canis familiaris	ENSCAFG00000001615	4 retrocopies	retro_cfam_184, retro_cfam_1936, retro_cfam_48, retro_cfam_87,
Callithrix jacchus	ENSCJAG00000020612	6 retrocopies	retro_cjac_1246, retro_cjac_18, retro_cjac_180, retro_cjac_190, retro_cjac_2982, retro_cjac_59,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Dasypus novemcinctus	ENSDNOG00000007241	1 retrocopy	retro_dnov_1192,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Microcebus murinus	ENSMICG00000007262	24 retrocopies	retro_mmur_1004, retro_mmur_1024, retro_mmur_1048, retro_mmur_1117, retro_mmur_1169, retro_mmur_1298, retro_mmur_1441, retro_mmur_1530, retro_mmur_189, retro_mmur_406, retro_mmur_414, retro_mmur_473, retro_mmur_517, retro_mmur_560, retro_mmur_723, retro_mmur_748, retro_mmur_760, retro_mmur_783, retro_mmur_794, retro_mmur_811, retro_mmur_856, retro_mmur_88, retro_mmur_907, retro_mmur_911,
Macaca mulatta	ENSMMUG00000003412	1 retrocopy	retro_mmul_263,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Mus musculus	ENSMUSG00000028495	45 retrocopies	retro_mmus_1010, retro_mmus_1126, retro_mmus_1291, retro_mmus_1357, retro_mmus_1436, retro_mmus_1590, retro_mmus_1663, retro_mmus_1701, retro_mmus_1720, retro_mmus_1966, retro_mmus_1969, retro_mmus_2047, retro_mmus_2068, retro_mmus_2146, retro_mmus_2167, retro_mmus_2171, retro_mmus_2336, retro_mmus_2342, retro_mmus_2367, retro_mmus_2369, retro_mmus_2489, retro_mmus_2546, retro_mmus_2593, retro_mmus_2601, retro_mmus_2625, retro_mmus_2824, retro_mmus_2845, retro_mmus_2946, retro_mmus_3154, retro_mmus_324, retro_mmus_3256, retro_mmus_3338, retro_mmus_3498, retro_mmus_3633, retro_mmus_475, retro_mmus_477 , retro_mmus_478, retro_mmus_568, retro_mmus_588, retro_mmus_617, retro_mmus_716, retro_mmus_743, retro_mmus_748, retro_mmus_895, retro_mmus_938,
Ochotona princeps	ENSOPRG00000000751	6 retrocopies	retro_opri_1111, retro_opri_1187, retro_opri_248, retro_opri_33, retro_opri_466, retro_opri_865,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Pongo abelii	ENSPPYG00000019193	15 retrocopies	retro_pabe_1024, retro_pabe_1625, retro_pabe_2065, retro_pabe_2616, retro_pabe_2617, retro_pabe_2882, retro_pabe_2964, retro_pabe_3282, retro_pabe_3481, retro_pabe_3777, retro_pabe_629, retro_pabe_730, retro_pabe_822, retro_pabe_850, retro_pabe_955,
Rattus norvegicus	ENSRNOG00000049025	8 retrocopies	retro_rnor_1008, retro_rnor_1189, retro_rnor_1988, retro_rnor_1990, retro_rnor_2085, retro_rnor_2635, retro_rnor_479, retro_rnor_718,
Vicugna pacos	ENSVPAG00000006030	10 retrocopies	retro_vpac_217, retro_vpac_228, retro_vpac_288, retro_vpac_297, retro_vpac_392, retro_vpac_407, retro_vpac_412, retro_vpac_438, retro_vpac_618, retro_vpac_70,