RetrogeneDB ID: retro_sscr_196

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:255051961..255052206(-)
• Located in intron of: ENSSSCG00000005273

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000023777
• Aliases: None
• Description: Sus scrofa ATP synthase, H+ transporting, mitochondrial Fo complex, subunit G (ATP5L), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001244137]

Sequence

>retro_sscr_196
GTCTGTAACCTTGTAGAGAAGGCCCAGGTGCTGGTCAATGCTGCTGTGACTTACTGGAAACCTCTCCTGGCCACAGTCTG
GCACTATGCCAAGGTTGAGCTGGTTCCTCCAGTCCCTGCTGAGATCCCTGCAGCTATTCAGAGCTTGAAAAACCTGTCAA
TAGTGCTCAGACTGGTAGCTTGAAACAGCTCACAGTTAAGAAAGCTCTGCTGAATTGTCTAGAGGCCACTGAGGTGTAGA
TGTAT

Alignment

ORF - retro_sscr_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.72 %
• Parental protein coverage: 79.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRNLAEKAPVLVNAAVTYSKPRLATFWHYAKVELVPPTPAEIPTAIQSLK-KIVNSAQTGSFKQLTVKEA
          V.NL.EKA.VLVNAAVTY.KP.LAT.WHYAKVELVPP.PAEIP.AIQSLK.K.VNSAQTGS.KQLTVK.A
Retrocopy VCNLVEKAQVLVNAAVTYWKPLLATVWHYAKVELVPPVPAEIPAAIQSLK<KPVNSAQTGSLKQLTVKKA

Parental  LLNGLVATEVLMW
          LLN.L.ATEV.M.
Retrocopy LLNCLEATEV*MY

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	76.32 RPM
SRP014902_testis	0.00 RPM	71.85 RPM
SRP018288_heart	0.03 RPM	330.98 RPM
SRP018288_kidney	0.00 RPM	361.02 RPM
SRP018288_liver	0.00 RPM	120.57 RPM
SRP018288_lung	0.10 RPM	49.59 RPM
SRP018856_adipose	0.00 RPM	74.76 RPM
SRP035408_brain	0.00 RPM	153.72 RPM
SRP035408_liver	0.06 RPM	112.11 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_196 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_196 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 127 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007332	2 retrocopies	retro_btau_105, retro_btau_245,
Choloepus hoffmanni	ENSCHOG00000010589	3 retrocopies	retro_chof_1454, retro_chof_1865, retro_chof_2204,
Callithrix jacchus	ENSCJAG00000013281	1 retrocopy	retro_cjac_283,
Dasypus novemcinctus	ENSDNOG00000019354	5 retrocopies	retro_dnov_1491, retro_dnov_1872, retro_dnov_2169, retro_dnov_2341, retro_dnov_344,
Equus caballus	ENSECAG00000023715	1 retrocopy	retro_ecab_434,
Erinaceus europaeus	ENSEEUG00000009863	7 retrocopies	retro_eeur_106, retro_eeur_111, retro_eeur_333, retro_eeur_495, retro_eeur_499, retro_eeur_589, retro_eeur_606,
Echinops telfairi	ENSETEG00000008755	11 retrocopies	retro_etel_1239, retro_etel_166, retro_etel_1884, retro_etel_1885, retro_etel_2183, retro_etel_241, retro_etel_254, retro_etel_355, retro_etel_822, retro_etel_876, retro_etel_995,
Felis catus	ENSFCAG00000011782	4 retrocopies	retro_fcat_1358, retro_fcat_1615, retro_fcat_1941, retro_fcat_371,
Homo sapiens	ENSG00000167283	5 retrocopies	retro_hsap_3029, retro_hsap_3110, retro_hsap_63, retro_hsap_860, retro_hsap_883,
Loxodonta africana	ENSLAFG00000030274	3 retrocopies	retro_lafr_1209, retro_lafr_135, retro_lafr_3,
Macropus eugenii	ENSMEUG00000015281	1 retrocopy	retro_meug_1774,
Microcebus murinus	ENSMICG00000015233	6 retrocopies	retro_mmur_1428, retro_mmur_237, retro_mmur_365, retro_mmur_513, retro_mmur_700, retro_mmur_725,
Macaca mulatta	ENSMMUG00000017604	4 retrocopies	retro_mmul_1333, retro_mmul_22, retro_mmul_25, retro_mmul_262,
Mus musculus	ENSMUSG00000038717	1 retrocopy	retro_mmus_139,
Nomascus leucogenys	ENSNLEG00000007362	6 retrocopies	retro_nleu_425, retro_nleu_608, retro_nleu_765, retro_nleu_81, retro_nleu_841, retro_nleu_846,
Oryctolagus cuniculus	ENSOCUG00000029455	4 retrocopies	retro_ocun_1140, retro_ocun_1156, retro_ocun_1418, retro_ocun_567,
Otolemur garnettii	ENSOGAG00000016298	10 retrocopies	retro_ogar_1097, retro_ogar_1102, retro_ogar_176, retro_ogar_3286, retro_ogar_3332, retro_ogar_352, retro_ogar_433, retro_ogar_444, retro_ogar_533, retro_ogar_573,
Pongo abelii	ENSPPYG00000003933	5 retrocopies	retro_pabe_1913, retro_pabe_2508, retro_pabe_2568, retro_pabe_2589, retro_pabe_688,
Pan troglodytes	ENSPTRG00000004342	5 retrocopies	retro_ptro_1518, retro_ptro_2043, retro_ptro_2102, retro_ptro_2478, retro_ptro_597,
Rattus norvegicus	ENSRNOG00000028884	19 retrocopies	retro_rnor_1145, retro_rnor_1160, retro_rnor_1185, retro_rnor_1319, retro_rnor_1345, retro_rnor_1379, retro_rnor_1420, retro_rnor_1468, retro_rnor_1993, retro_rnor_2258, retro_rnor_2271, retro_rnor_2404, retro_rnor_2573, retro_rnor_2650, retro_rnor_2723, retro_rnor_2735, retro_rnor_2929, retro_rnor_660, retro_rnor_698,
Sus scrofa	ENSSSCG00000023777	5 retrocopies	retro_sscr_196 , retro_sscr_270, retro_sscr_378, retro_sscr_463, retro_sscr_500,
Ictidomys tridecemlineatus	ENSSTOG00000014400	2 retrocopies	retro_itri_1649, retro_itri_332,
Tupaia belangeri	ENSTBEG00000009999	4 retrocopies	retro_tbel_1364, retro_tbel_4005, retro_tbel_857, retro_tbel_959,
Tarsius syrichta	ENSTSYG00000002686	4 retrocopies	retro_tsyr_1516, retro_tsyr_1688, retro_tsyr_2166, retro_tsyr_578,
Tursiops truncatus	ENSTTRG00000004284	9 retrocopies	retro_ttru_1088, retro_ttru_1125, retro_ttru_1255, retro_ttru_1537, retro_ttru_1781, retro_ttru_541, retro_ttru_716, retro_ttru_810, retro_ttru_972,