RetrogeneDB ID: retro_sscr_610

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:2216525..2216940(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSSSCG00000012459
• Aliases: None
• Description: None

Sequence

>retro_sscr_610
GTGACAGCTTTCAGGATGGGAGAGTGGACAACCATGGCAGCAGGCCTAATAGTTGCATCTGTAAAAGGGCACGCGGCCAA
AGAGGAGGACGCCAAAAAGCAGCTAATGAAACCCGAGCAGCTCCCCATAACTACCAAACCACCTCTTCGGTCTAGATACG
CTGAAGAGCAGCCGGGATGTTTACCAAGGGCTTTGAGTCCACTCCACTGCCACGGGTCGTTACTTTGGCTGGTGCAAGGG
TGTTTCTGTCTTTGTGAAAAATAGGAGCACAGGTGCAGTACAATTTGGAAAAGGTGGATGTGTCTATGCGAAGAATCCGC
CTGGAAACGTTCTTCCAAAAATGGGAGGGATTTCAGCTTCAGCATTGGTGGGCTTCGTTTCTGCGAGAAGAGGTTCTAGG
TTTAGGAAAATTGCT

Alignment

ORF - retro_sscr_610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.41 %
• Parental protein coverage: 51.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAFRMRKLTTMPVGLICASVSVHVAKEEESRKQLVKPEQLPIYTAPPLQSKYVEEQPGRLQ-VGFASI-
          ..AFRM...TTM..GLI.ASV..H.AKEE...KQL.KPEQLPI.T.PPL.S.Y.EEQPG.L...GF.S..
Retrocopy VTAFRMGEWTTMAAGLIVASVKGHAAKEEDAKKQLMKPEQLPITTKPPLRSRYAEEQPGCLP<KGFEST<

Parental  RTTTGRYLGWCKSAYVFMKNGIKDAVQFGKDAYVYLKNPPRDFLPKIGVITVSGLAGFVSARKGSRFKKI
          .T.TGRY.GWCK...VF.KN....AVQFGK...VY.KNPP...LPK.G.I..S.L.GFVSAR.GSRF.KI
Retrocopy STATGRYFGWCKGVSVFVKNRSTGAVQFGKGGCVYAKNPPGNVLPKMGGISASALVGFVSARRGSRFRKI

Parental  A
          A
Retrocopy A

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	3.72 RPM
SRP014902_testis	0.00 RPM	4.81 RPM
SRP018288_heart	0.00 RPM	28.11 RPM
SRP018288_kidney	0.00 RPM	21.97 RPM
SRP018288_liver	0.00 RPM	12.15 RPM
SRP018288_lung	0.00 RPM	4.58 RPM
SRP018856_adipose	0.00 RPM	6.55 RPM
SRP035408_brain	0.00 RPM	4.80 RPM
SRP035408_liver	0.00 RPM	22.66 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_610 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_610 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012174	1 retrocopy	retro_sscr_774,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610 ,
Tupaia belangeri	ENSTBEG00000010147	5 retrocopies	retro_tbel_2037, retro_tbel_2609, retro_tbel_2840, retro_tbel_3361, retro_tbel_3737,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,