RetrogeneDB ID: retro_mmus_114

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:9283378..9284164(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000067608
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Pcna
• Ensembl ID: ENSMUSG00000027342
• Aliases: None
• Description: proliferating cell nuclear antigen [Source:MGI Symbol;Acc:MGI:97503]

Sequence

>retro_mmus_114
ATGTTTGAGGCACGCCTGATCCAGGGCTCCATCCTGAAGAAGGTGCTGGAGGCTCTCAAAGACCTCATCAATGAGGCCTG
CTGGGACGTCAGCTCGGGCGGCGTGAACCTGCAGAGCATGGACTCGTCTCACGTCTCCTTGGTGCAGCTTACTCTGCGCT
CCGAAGGCTTCGACACCTACCGCTGCGACCGCAACCTAGCCATGGGCGTGAACCTCACCAGCATGTCCAAAATTCTAAAA
TGTGCTGGTAATGAAGACATCATTACATTAAGGGCTGAAGATAATGCAGACACCTTAGCACTAGTATTCGAAGCACCAAA
TCAAGAGAAAGTTTCAGACTATGAAATGAAGTTAATGGACTTAGATGTGGAGCAACTTGGAATCCCAGAACAGGAGTACA
GCTGTGTAATAAAGATGCCGTCGAGTGAATTTGCACGTATATGCCGAGACCTTAGCCACATTGGAGATGCTGTTGTGATA
TCCTGTGCAAAGAATGGGGTGAAGTTTTCTGCAAGTGGAGAGCTTGGCAATGGGAACATTAAGTTGTCACAAACAAGTAA
TGTGGATAAAGAAGAGGAGGCGGTAGCCATAGAGATGAATGAGCCTGTTCACCTAACTTTTGCTCTGAGGTACCTGAACT
TTTTCACAAAAGCCACTCCACTGTCTCCTACAGTAACACTCAGTATGTCTGCAGATGTACCCCTTGTTGTAGAGTATAAA
ATTGCTGACATGGGACACTTAAAGTATTATTTGGCTCCCAAGATTGAAGATGAGGAAGCATCTTAG

Alignment

ORF - retro_mmus_114 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFEARLIQGSILKKVLEALKDLINEACWDVSSGGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGV
          MFEARLIQGSILKKVLEALKDLINEACWDVSSGGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGV
Retrocopy MFEARLIQGSILKKVLEALKDLINEACWDVSSGGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGV

Parental  NLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVIKMP
          NLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVIKMP
Retrocopy NLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVIKMP

Parental  SGEFARICRDLSHIGDAVVISCAKNGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVHLTFALR
          S.EFARICRDLSHIGDAVVISCAKNGVKFSASGELGNGNIKLSQTSNVDKEEEAV.IEMNEPVHLTFALR
Retrocopy SSEFARICRDLSHIGDAVVISCAKNGVKFSASGELGNGNIKLSQTSNVDKEEEAVAIEMNEPVHLTFALR

Parental  YLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEAS
          YLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEAS
Retrocopy YLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEAS

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	0.14 RPM	18.97 RPM
SRP007412_cerebellum	0.04 RPM	20.67 RPM
SRP007412_heart	0.03 RPM	20.61 RPM
SRP007412_kidney	0.17 RPM	23.89 RPM
SRP007412_liver	0.05 RPM	19.99 RPM
SRP007412_testis	0.23 RPM	63.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_114 was not detected

EST

No EST(s) were mapped for retro_mmus_114 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_67925	369 libraries	141 libraries	415 libraries	134 libraries	13 libraries
TSS #2	TSS_67926	367 libraries	461 libraries	237 libraries	5 libraries	2 libraries

The graphical summary, for retro_mmus_114 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_114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_114 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009089	1 retrocopy	retro_amel_1719,
Canis familiaris	ENSCAFG00000006030	2 retrocopies	retro_cfam_1626, retro_cfam_946,
Callithrix jacchus	ENSCJAG00000021278	3 retrocopies	retro_cjac_2159, retro_cjac_2175, retro_cjac_930,
Cavia porcellus	ENSCPOG00000009242	1 retrocopy	retro_cpor_315,
Erinaceus europaeus	ENSEEUG00000003069	1 retrocopy	retro_eeur_358,
Echinops telfairi	ENSETEG00000006577	3 retrocopies	retro_etel_1152, retro_etel_1539, retro_etel_2217,
Felis catus	ENSFCAG00000009068	2 retrocopies	retro_fcat_1363, retro_fcat_1729,
Homo sapiens	ENSG00000132646	3 retrocopies	retro_hsap_3067, retro_hsap_4817, retro_hsap_857,
Gorilla gorilla	ENSGGOG00000001695	2 retrocopies	retro_ggor_2107, retro_ggor_700,
Myotis lucifugus	ENSMLUG00000001693	1 retrocopy	retro_mluc_1658,
Macaca mulatta	ENSMMUG00000013259	3 retrocopies	retro_mmul_1059, retro_mmul_1960, retro_mmul_2570,
Monodelphis domestica	ENSMODG00000011649	1 retrocopy	retro_mdom_933,
Mustela putorius furo	ENSMPUG00000006195	2 retrocopies	retro_mputfur_330, retro_mputfur_629,
Mus musculus	ENSMUSG00000027342	1 retrocopy	retro_mmus_114 ,
Nomascus leucogenys	ENSNLEG00000007726	2 retrocopies	retro_nleu_2192, retro_nleu_424,
Otolemur garnettii	ENSOGAG00000033161	2 retrocopies	retro_ogar_1258, retro_ogar_2960,
Procavia capensis	ENSPCAG00000010500	1 retrocopy	retro_pcap_130,
Pongo abelii	ENSPPYG00000010795	3 retrocopies	retro_pabe_2542, retro_pabe_3745, retro_pabe_690,
Pan troglodytes	ENSPTRG00000013222	3 retrocopies	retro_ptro_2068, retro_ptro_3206, retro_ptro_595,
Pteropus vampyrus	ENSPVAG00000002865	1 retrocopy	retro_pvam_193,
Rattus norvegicus	ENSRNOG00000021264	1 retrocopy	retro_rnor_1035,
Sorex araneus	ENSSARG00000004070	1 retrocopy	retro_sara_640,
Sus scrofa	ENSSSCG00000030642	1 retrocopy	retro_sscr_113,
Tursiops truncatus	ENSTTRG00000015368	2 retrocopies	retro_ttru_1868, retro_ttru_440,