RetrogeneDB ID: retro_sscr_780

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:55555854..55556096(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000002907
• Aliases: None
• Description: Sus scrofa COX6B protein (COX6B), mRNA. [Source:RefSeq mRNA;Acc:NM_001097497]

Sequence

>retro_sscr_780
ATGATAGAAGATATTAAGACCAAAATCAAGAACCAACAGACTGTCCCTTTGACAGACCCTTCCCCAACCAGAACCAGACT
AGAGCAGCTGGCAGAAAGCCCTGGACTTCCTGTGAGGAAGCAATGACAGGTAAAAGGGGTGACTGTCTCCAGGTGTGAAT
TAGACCACATGTACAAGTCCCTCAGCCCCATATCTTGGGTATCAGCCTAGGACAACCACAGGCACAAGGCACATTTCCTG
GG

Alignment

ORF - retro_sscr_780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.32 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAEDIQTKIKNYQTAP-FDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGD-VSVCEWYRRVYKSLCPIS
          M.EDI.TKIKN.QT.P.FD..FP..NQ.............CE.AMT.K.GD.VS.CE.....YKSL.PIS
Retrocopy MIEDIKTKIKNQQTVP<FDRPFP--NQNQTRAAGRKPWTSCEEAMTGKRGD>VSRCE-LDHMYKSLSPIS

Parental  WVSAWDDRR-AEGTFPG
          WVSA.D..R.A.GTFPG
Retrocopy WVSA*DNHR<AQGTFPG

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	103.80 RPM
SRP014902_testis	0.00 RPM	44.70 RPM
SRP018288_heart	0.00 RPM	328.70 RPM
SRP018288_kidney	0.00 RPM	178.49 RPM
SRP018288_liver	0.00 RPM	79.48 RPM
SRP018288_lung	0.00 RPM	42.87 RPM
SRP018856_adipose	0.00 RPM	114.89 RPM
SRP035408_brain	0.00 RPM	194.95 RPM
SRP035408_liver	0.00 RPM	130.75 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_780 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_780 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000563	3 retrocopies	retro_amel_1653, retro_amel_581, retro_amel_775,
Canis familiaris	ENSCAFG00000006913	7 retrocopies	retro_cfam_1614, retro_cfam_1760, retro_cfam_517, retro_cfam_6, retro_cfam_775, retro_cfam_830, retro_cfam_929,
Callithrix jacchus	ENSCJAG00000010211	5 retrocopies	retro_cjac_1513, retro_cjac_2007, retro_cjac_268, retro_cjac_2870, retro_cjac_2924,
Equus caballus	ENSECAG00000012317	3 retrocopies	retro_ecab_1051, retro_ecab_190, retro_ecab_719,
Felis catus	ENSFCAG00000006378	5 retrocopies	retro_fcat_107, retro_fcat_2017, retro_fcat_293, retro_fcat_758, retro_fcat_783,
Homo sapiens	ENSG00000126267	5 retrocopies	retro_hsap_1762, retro_hsap_2906, retro_hsap_3807, retro_hsap_4032, retro_hsap_4089,
Microcebus murinus	ENSMICG00000009902	5 retrocopies	retro_mmur_1099, retro_mmur_1413, retro_mmur_1588, retro_mmur_77, retro_mmur_809,
Myotis lucifugus	ENSMLUG00000011365	4 retrocopies	retro_mluc_2244, retro_mluc_2455, retro_mluc_55, retro_mluc_933,
Macaca mulatta	ENSMMUG00000016765	5 retrocopies	retro_mmul_1212, retro_mmul_1227, retro_mmul_1655, retro_mmul_1989, retro_mmul_2327,
Monodelphis domestica	ENSMODG00000013962	1 retrocopy	retro_mdom_1046,
Mustela putorius furo	ENSMPUG00000006258	1 retrocopy	retro_mputfur_998,
Mus musculus	ENSMUSG00000036751	1 retrocopy	retro_mmus_2498,
Nomascus leucogenys	ENSNLEG00000011283	5 retrocopies	retro_nleu_1914, retro_nleu_2396, retro_nleu_2829, retro_nleu_2845, retro_nleu_978,
Oryctolagus cuniculus	ENSOCUG00000009606	2 retrocopies	retro_ocun_1797, retro_ocun_840,
Otolemur garnettii	ENSOGAG00000004148	4 retrocopies	retro_ogar_1903, retro_ogar_3033, retro_ogar_3447, retro_ogar_553,
Oryzias latipes	ENSORLG00000006070	1 retrocopy	retro_olat_4,
Pan troglodytes	ENSPTRG00000010854	4 retrocopies	retro_ptro_1209, retro_ptro_1964, retro_ptro_2583, retro_ptro_2733,
Pteropus vampyrus	ENSPVAG00000012821	8 retrocopies	retro_pvam_1031, retro_pvam_1044, retro_pvam_1331, retro_pvam_303, retro_pvam_336, retro_pvam_576, retro_pvam_717, retro_pvam_757,
Rattus norvegicus	ENSRNOG00000024309	1 retrocopy	retro_rnor_201,
Sorex araneus	ENSSARG00000010771	1 retrocopy	retro_sara_51,
Sus scrofa	ENSSSCG00000002907	2 retrocopies	retro_sscr_780 , retro_sscr_89,
Tarsius syrichta	ENSTSYG00000014563	8 retrocopies	retro_tsyr_1179, retro_tsyr_1257, retro_tsyr_1260, retro_tsyr_1897, retro_tsyr_44, retro_tsyr_486, retro_tsyr_78, retro_tsyr_80,
Tursiops truncatus	ENSTTRG00000002241	2 retrocopies	retro_ttru_619, retro_ttru_94,