RetrogeneDB ID: retro_sscr_774

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:39585571..39585903(-)
• Located in intron of: ENSSSCG00000006066

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOO
• Ensembl ID: ENSSSCG00000012174
• Aliases: None
• Description: apolipoprotein O [Source:HGNC Symbol;Acc:28727]

Sequence

>retro_sscr_774
TCCAATCTCTAACATTATTGCGAACCACATACAAGTTGGTGTCAGGACATGTACTCCCAAACTAAGCCCAAGATGCAAAG
TTTGGTTCAATAGGGATTAGACAGCTATGAATATCTCCAAAATGCACCCTCCTGGATTTTTTCCAAGGCTTGGTATTAAC
TGGTTTTGCTGGGGTTGTTGGACTTCTTTTGGCTGGAGGTTCAAAAATAAAGAAACTGGTGTAACCACCTGGTTTCATGG
GATTAGCTGCCTCTCTTTATCATCCACAACAAGCCCAGGTCAGTGGAGAGAAATTATATGACTAGGGTTTACGAGGATAC
ACAGTCATAGAA

Alignment

ORF - retro_sscr_774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.62 %
• Parental protein coverage: 57.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHLRHYCEPYTSWCQEMYSQTKPKMQSLVQWGLDSYEYLQNA-PPGFFPRLGV-IGFAGVVGLLLARGSK
          S.L.HYCEP.TSWCQ.MYSQTKPKMQSLVQ.GLDSYEYLQNA.PPGFFPRLG...GFAGVVGLLLA.GSK
Retrocopy SNL*HYCEPHTSWCQDMYSQTKPKMQSLVQ*GLDSYEYLQNA>PPGFFPRLGI>TGFAGVVGLLLAGGSK

Parental  IKKLVYPPGFMGLAASLYYPQQAIVFAQVSGEKLYDWGLRGYIVVE
          IKKLV.PPGFMGLAASLY.PQQA....QVSGEKLYD.GLRGY.V.E
Retrocopy IKKLV*PPGFMGLAASLYHPQQA----QVSGEKLYD*GLRGYTVIE

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	2.52 RPM
SRP014902_testis	0.00 RPM	6.51 RPM
SRP018288_heart	0.03 RPM	31.04 RPM
SRP018288_kidney	0.00 RPM	23.94 RPM
SRP018288_liver	0.16 RPM	4.16 RPM
SRP018288_lung	0.20 RPM	1.93 RPM
SRP018856_adipose	0.14 RPM	2.82 RPM
SRP035408_brain	0.06 RPM	13.37 RPM
SRP035408_liver	0.00 RPM	4.70 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_774 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_774 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012749	1 retrocopy	retro_amel_1282,
Choloepus hoffmanni	ENSCHOG00000000226	2 retrocopies	retro_chof_2372, retro_chof_839,
Callithrix jacchus	ENSCJAG00000004909	8 retrocopies	retro_cjac_1360, retro_cjac_1417, retro_cjac_1448, retro_cjac_1767, retro_cjac_1792, retro_cjac_1896, retro_cjac_2038, retro_cjac_2063,
Cavia porcellus	ENSCPOG00000004197	1 retrocopy	retro_cpor_309,
Dasypus novemcinctus	ENSDNOG00000006710	1 retrocopy	retro_dnov_2450,
Equus caballus	ENSECAG00000013441	1 retrocopy	retro_ecab_145,
Echinops telfairi	ENSETEG00000014150	3 retrocopies	retro_etel_1052, retro_etel_516, retro_etel_711,
Felis catus	ENSFCAG00000000029	3 retrocopies	retro_fcat_1203, retro_fcat_1657, retro_fcat_1798,
Homo sapiens	ENSG00000184831	5 retrocopies	retro_hsap_1018, retro_hsap_1693, retro_hsap_2670, retro_hsap_3047, retro_hsap_3259,
Gorilla gorilla	ENSGGOG00000001200	4 retrocopies	retro_ggor_1269, retro_ggor_1863, retro_ggor_2098, retro_ggor_806,
Loxodonta africana	ENSLAFG00000029070	1 retrocopy	retro_lafr_1114,
Macropus eugenii	ENSMEUG00000014222	1 retrocopy	retro_meug_700,
Macaca mulatta	ENSMMUG00000016361	4 retrocopies	retro_mmul_1584, retro_mmul_1886, retro_mmul_2051, retro_mmul_814,
Monodelphis domestica	ENSMODG00000025554	1 retrocopy	retro_mdom_1510,
Mustela putorius furo	ENSMPUG00000000109	1 retrocopy	retro_mputfur_109,
Mus musculus	ENSMUSG00000079508	1 retrocopy	retro_mmus_282,
Nomascus leucogenys	ENSNLEG00000010026	5 retrocopies	retro_nleu_1167, retro_nleu_1338, retro_nleu_1944, retro_nleu_456, retro_nleu_898,
Otolemur garnettii	ENSOGAG00000001960	6 retrocopies	retro_ogar_1083, retro_ogar_1104, retro_ogar_2092, retro_ogar_2466, retro_ogar_2927, retro_ogar_3094,
Pongo abelii	ENSPPYG00000020191	7 retrocopies	retro_pabe_1394, retro_pabe_1417, retro_pabe_2215, retro_pabe_2417, retro_pabe_2434, retro_pabe_2702, retro_pabe_856,
Pan troglodytes	ENSPTRG00000021742	5 retrocopies	retro_ptro_1147, retro_ptro_1799, retro_ptro_1992, retro_ptro_2205, retro_ptro_746,
Pteropus vampyrus	ENSPVAG00000002530	2 retrocopies	retro_pvam_128, retro_pvam_594,
Rattus norvegicus	ENSRNOG00000046918	4 retrocopies	retro_rnor_1022, retro_rnor_1986, retro_rnor_2096, retro_rnor_2308,
Sarcophilus harrisii	ENSSHAG00000008734	1 retrocopy	retro_shar_125,
Sus scrofa	ENSSSCG00000012174	1 retrocopy	retro_sscr_774 ,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tupaia belangeri	ENSTBEG00000014888	6 retrocopies	retro_tbel_1153, retro_tbel_4004, retro_tbel_4261, retro_tbel_4698, retro_tbel_715, retro_tbel_96,
Tarsius syrichta	ENSTSYG00000010239	2 retrocopies	retro_tsyr_1089, retro_tsyr_2155,