RetrogeneDB ID: retro_sscr_113

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:75328581..75329202(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCNA
• Ensembl ID: ENSSSCG00000030642
• Aliases: None
• Description: proliferating cell nuclear antigen [Source:HGNC Symbol;Acc:8729]

Sequence

>retro_sscr_113
GAGGGCTTCCACACGTACTGCTGCGACCGCAATTTGGCCATAGGTGTGAACCTCACCAGCATGTCCAAAACACTAAAATG
TGCTGGCAATGAAGACATCATTACACTAAGGGTTGAAGATAAGGCAGACACCTTGGCACTAGTGTTTGAAGCTCCAAATC
AAGAAAAGGTTTCAGCCTATGAAATGAAGTTAATGAATTTAGATGTTGAGCAACTTGGAATTCCCGAACAAGAGTACAGC
TGTGTAGTAAAGATGCCTTCTGGTGAGTTTGCATGTATATACCGAGATCTCAGTCATATTGGAGATGCCGTTGTAATTTC
CTGTGCAAAAGATGGAGTGAAATTTTCTGCAAGTGGAGAACTTGGAAATGGAAATGCTAAGTTGTCACAAATGAGTAATG
TTGATAAAGAGGAGGAAGCTGTTACCATAGAGATGAATGAACCAGTTCAGCTAACTTTTGCACTGAGGTACCTGAACTTC
TTCACAAAAGCCATTCCACTCTCTCCTACAGTAACACTCAGTATGTCTGCAGATGTACCCCTTGTTGTAGAGTATAAAAT
TGCTGATATGGGACATTTAAAGCACTATTTGGCTCCCAAGATCGAAGATGAAGAAGGCTCT

Alignment

ORF - retro_sscr_113 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 79.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVE
          EGF.TY.CDRNLA.GVNLTSMSK.LKCAGNEDIITLR.ED.ADTLALVFEAPNQEKVS.YEMKLM.LDVE
Retrocopy EGFHTYCCDRNLAIGVNLTSMSKTLKCAGNEDIITLRVEDKADTLALVFEAPNQEKVSAYEMKLMNLDVE

Parental  QLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEA
          QLGIPEQEYSCVVKMPSGEFA.I.RDLSHIGDAVVISCAKDGVKFSASGELGNGN.KLSQ.SNVDKEEEA
Retrocopy QLGIPEQEYSCVVKMPSGEFACIYRDLSHIGDAVVISCAKDGVKFSASGELGNGNAKLSQMSNVDKEEEA

Parental  VTIEMNEPVQLTFALRYLNFFTKATPLSPTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGS
          VTIEMNEPVQLTFALRYLNFFTKA.PLSPTVTLSMSADVPLVVEYKIADMGHLK.YLAPKIEDEEGS
Retrocopy VTIEMNEPVQLTFALRYLNFFTKAIPLSPTVTLSMSADVPLVVEYKIADMGHLKHYLAPKIEDEEGS

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
SRP014902_placenta	0.00 RPM	13.27 RPM
SRP014902_testis	0.00 RPM	45.40 RPM
SRP018288_heart	0.00 RPM	27.37 RPM
SRP018288_kidney	0.00 RPM	51.91 RPM
SRP018288_liver	0.00 RPM	23.03 RPM
SRP018288_lung	0.51 RPM	53.26 RPM
SRP018856_adipose	0.00 RPM	18.63 RPM
SRP035408_brain	0.00 RPM	19.47 RPM
SRP035408_liver	0.03 RPM	53.19 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_113 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_113 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_113 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,