RetrogeneDB ID: retro_sscr_558

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:77000012..77000414(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000017077
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSSSCG00000010953
• Aliases: None
• Description: iron-sulfur cluster assembly 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28660]

Sequence

>retro_sscr_558
GTTGCTGGGATGGTGAAGATGTTGGCTTCATTAGTCTGGGCCACTGTCCAGTCTGTGAGCAAGAGGAAGCTGCAGCCCAC
CTGGGCTGCCCTCACCATGACACCTTCAGCAAATGAGATAAAACAACTTCTTAGAGATAAGCCTGAACTCGTAGGTGTGA
AAGTTGGTGTCCGAACCAGGGGTTGTAATGGCCTTTCCTACACTCTAGAATACACGAAGACAAAAGGAGACTCTGATGAA
GAAGTTGTTCAAGATGGAGTCAGAGTGTTCATTGAGAAGAAAGCACAGCTAACACTTTTAGGAACAGAAATGGACTATGT
TGAAGACAAATTATCCAGTGAGTTTGTGTTCAATAACCCAAACCTCAAAGGAACATGGGGCTGTGGAGAAAGCTTTAATA
TC

Alignment

ORF - retro_sscr_558 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 79.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAGTAKMSASLVRATVRAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGVKVGVRTRGCNGLSYTL
          VAG..KM.ASLV.ATV..VSKRKLQPT.AALT.TPSA.N.IKQLL.DKPE.VGVKVGVRTRGCNGLSYTL
Retrocopy VAGMVKMLASLVWATVQSVSKRKLQPTWAALTMTPSA-NEIKQLLRDKPELVGVKVGVRTRGCNGLSYTL

Parental  EYTKTKGDSDEEVVQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFNI
          EYTKTKGDSDEEVVQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPN.KGT.GCGESFNI
Retrocopy EYTKTKGDSDEEVVQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNLKGTWGCGESFNI

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	19.64 RPM
SRP014902_testis	0.14 RPM	37.77 RPM
SRP018288_heart	0.24 RPM	153.55 RPM
SRP018288_kidney	0.00 RPM	54.28 RPM
SRP018288_liver	0.16 RPM	43.18 RPM
SRP018288_lung	0.00 RPM	34.72 RPM
SRP018856_adipose	0.00 RPM	35.79 RPM
SRP035408_brain	0.00 RPM	39.89 RPM
SRP035408_liver	0.00 RPM	34.70 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_558 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Canis familiaris	ENSCAFG00000001336	1 retrocopy	retro_cfam_1087,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Equus caballus	ENSECAG00000011465	1 retrocopy	retro_ecab_936,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Pteropus vampyrus	ENSPVAG00000004588	1 retrocopy	retro_pvam_956,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Sus scrofa	ENSSSCG00000010953	1 retrocopy	retro_sscr_558 ,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,
Tursiops truncatus	ENSTTRG00000004231	1 retrocopy	retro_ttru_1317,