RetrogeneDB ID: retro_sscr_562

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 17:8459024..8459388(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX5B
• Ensembl ID: ENSSSCG00000008195
• Aliases: None
• Description: Sus scrofa mitochondrial cytochrome c oxidase subunit Vb (Cox5b), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001007517]

Sequence

>retro_sscr_562
TCACGATTACTTTGCAGAACTGAAACACTGGCTGGCGAAGGCCCTGAGGGCCCACAGTCCCAGTGGGATTGCAGCAGTGT
GCTCCATGGCATCTGGAGGTAGTTTTCCTACTGATGAGAAGCAGACAGCTGGGCTGGAGAGGAGAGCATGATGGCTTCAT
GGAAGGGATTGGACCCACTTAATATGCTATAGCCCCAAAGGCAGCTTCAGGCACCAAGAAAGACCCTCATTCTCCTCCAG
CACCAACAAGTGAATAGTGTGCTGCATCTGTGAGGAAGACAACAGTGCCGCCATCTCATTCCGGCTGCACAAAGGTGTGT
TTCATCGATGCCCTAAATGTGGAATCTACAGACTGGTGTCCTAC

Alignment

ORF - retro_sscr_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.59 %
• Parental protein coverage: 95.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SRLLRGAGALA-AQTLRARGPNGVAVVRSMASGGGVPTDEEQATGLER-EVMMAARK-GLDPY-NILAPK
          SRLL.....LA.A..LRA..P.G.A.V.SMASGG..PTDE.Q..GLER.E.MMA..K.G..P.....APK
Retrocopy SRLLCRTETLA>AKALRAHSPSGIAAVCSMASGGSFPTDEKQTAGLER<ESMMASWK<GIGPT*YAIAPK

Parental  AASGTK-EDPNLVPSITNKRIVGCICEEDNSTVIWFWVHKGETQRCPSCGTHYKLVSH
          AASGTK.E.P....S.TNK.IV.CICEEDNS..I.F..HKG...RCP.CG..Y.LVS.
Retrocopy AASGTK<ERPSFSSS-TNK*IVCCICEEDNSAAISFRLHKGVFHRCPKCGI-YRLVSY

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	149.32 RPM
SRP014902_testis	0.28 RPM	102.55 RPM
SRP018288_heart	0.00 RPM	372.13 RPM
SRP018288_kidney	0.00 RPM	349.01 RPM
SRP018288_liver	0.00 RPM	156.87 RPM
SRP018288_lung	0.00 RPM	46.94 RPM
SRP018856_adipose	0.00 RPM	231.38 RPM
SRP035408_brain	0.00 RPM	175.19 RPM
SRP035408_liver	0.00 RPM	160.17 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_562 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_562 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_712
Equus caballus	retro_ecab_674

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 112 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005242	7 retrocopies	retro_amel_1546, retro_amel_1583, retro_amel_1744, retro_amel_1867, retro_amel_536, retro_amel_65, retro_amel_746,
Bos taurus	ENSBTAG00000018542	2 retrocopies	retro_btau_1018, retro_btau_1651,
Canis familiaris	ENSCAFG00000002387	8 retrocopies	retro_cfam_1231, retro_cfam_1284, retro_cfam_1307, retro_cfam_1494, retro_cfam_1779, retro_cfam_2130, retro_cfam_398, retro_cfam_712,
Callithrix jacchus	ENSCJAG00000016911	6 retrocopies	retro_cjac_1679, retro_cjac_2119, retro_cjac_2477, retro_cjac_3096, retro_cjac_495, retro_cjac_505,
Dipodomys ordii	ENSDORG00000014994	3 retrocopies	retro_dord_246, retro_dord_360, retro_dord_72,
Equus caballus	ENSECAG00000007968	3 retrocopies	retro_ecab_189, retro_ecab_674, retro_ecab_762,
Erinaceus europaeus	ENSEEUG00000000258	1 retrocopy	retro_eeur_402,
Felis catus	ENSFCAG00000001704	7 retrocopies	retro_fcat_1572, retro_fcat_1795, retro_fcat_1961, retro_fcat_331, retro_fcat_568, retro_fcat_600, retro_fcat_776,
Homo sapiens	ENSG00000135940	7 retrocopies	retro_hsap_1295, retro_hsap_270, retro_hsap_3058, retro_hsap_3667, retro_hsap_3908, retro_hsap_903, retro_hsap_997,
Gorilla gorilla	ENSGGOG00000001142	6 retrocopies	retro_ggor_2101, retro_ggor_2479, retro_ggor_2635, retro_ggor_317, retro_ggor_730, retro_ggor_796,
Loxodonta africana	ENSLAFG00000009386	2 retrocopies	retro_lafr_605, retro_lafr_696,
Macropus eugenii	ENSMEUG00000005855	2 retrocopies	retro_meug_1202, retro_meug_1712,
Myotis lucifugus	ENSMLUG00000014512	1 retrocopy	retro_mluc_336,
Mustela putorius furo	ENSMPUG00000011327	8 retrocopies	retro_mputfur_1412, retro_mputfur_1528, retro_mputfur_1559, retro_mputfur_367, retro_mputfur_811, retro_mputfur_851, retro_mputfur_871, retro_mputfur_983,
Mus musculus	ENSMUSG00000061518	1 retrocopy	retro_mmus_59,
Nomascus leucogenys	ENSNLEG00000011668	5 retrocopies	retro_nleu_114, retro_nleu_1143, retro_nleu_1652, retro_nleu_380, retro_nleu_871,
Oryctolagus cuniculus	ENSOCUG00000017085	2 retrocopies	retro_ocun_1639, retro_ocun_508,
Otolemur garnettii	ENSOGAG00000016840	3 retrocopies	retro_ogar_1136, retro_ogar_1365, retro_ogar_2269,
Ochotona princeps	ENSOPRG00000002030	3 retrocopies	retro_opri_1128, retro_opri_334, retro_opri_568,
Pongo abelii	ENSPPYG00000012078	6 retrocopies	retro_pabe_1074, retro_pabe_1907, retro_pabe_2532, retro_pabe_3184, retro_pabe_399, retro_pabe_778,
Pan troglodytes	ENSPTRG00000012257	7 retrocopies	retro_ptro_1983, retro_ptro_226, retro_ptro_2488, retro_ptro_2658, retro_ptro_623, retro_ptro_754, retro_ptro_887,
Rattus norvegicus	ENSRNOG00000016660	2 retrocopies	retro_rnor_2740, retro_rnor_2741,
Sorex araneus	ENSSARG00000011275	1 retrocopy	retro_sara_579,
Sarcophilus harrisii	ENSSHAG00000017358	3 retrocopies	retro_shar_656, retro_shar_793, retro_shar_797,
Sus scrofa	ENSSSCG00000008195	4 retrocopies	retro_sscr_306, retro_sscr_562 , retro_sscr_757, retro_sscr_893,
Ictidomys tridecemlineatus	ENSSTOG00000010980	3 retrocopies	retro_itri_1185, retro_itri_848, retro_itri_94,
Tupaia belangeri	ENSTBEG00000012130	4 retrocopies	retro_tbel_1170, retro_tbel_2821, retro_tbel_3647, retro_tbel_3684,
Tursiops truncatus	ENSTTRG00000013490	5 retrocopies	retro_ttru_1438, retro_ttru_253, retro_ttru_270, retro_ttru_596, retro_ttru_790,