RetrogeneDB ID: retro_sscr_557

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:76448058..76448378(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA2
• Ensembl ID: ENSSSCG00000022365
• Aliases: None
• Description: pyrophosphatase (inorganic) 2 [Source:HGNC Symbol;Acc:28883]

Sequence

>retro_sscr_557
GTAGAAGTACCTCGGTGGACAAATGCTAAAAGGGAGATTGCCATGGAAGAGCCACTGAATCCTGTAAACAAGATGGAAAT
GAGGCCAAGCTTTGCTGTATGACAAGTATCTTTCCTCACAAGGGTCACATGTGGAGTTAGGGTGGCCTCCCTCAGACTTA
GGAGGACTCCTGTTGAAAAGAGAAGAGTGCAGACTGCTGTGGAGATAATAATCCTGTTGACCTTTGTGAAACAGGTGCAA
AGGTTCTTTCTCTTGGAGATGTTGTTCATGTGAAGAGCCTTGCAACTTTGGTTCTTATAGATCAGAGTGAAACAGATTGG

Alignment

ORF - retro_sscr_557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.74 %
• Parental protein coverage: 97.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEVPRWTNAKMEIATEEPLNPI-KQDVKNGKLRYVANIFPHKGYIWNYGALPQTWEDPHRKDESTDCCGD
          VEVPRWTNAK.EIA.EEPLNP..KQD....KL.....IFPHKG..W..G.LPQT.ED...K..S.DCCGD
Retrocopy VEVPRWTNAKREIAMEEPLNPV<KQDGNEAKLCCMTSIFPHKGHMWS*GGLPQT*EDSC*KEKSADCCGD

Parental  NDPIDVCEIGSKVLSRGEVVHVKILGILALIDQGETDW
          N.P.D.CE.G.KVLS.G.VVHVK.L..L.LIDQ.ETDW
Retrocopy NNPVDLCETGAKVLSLGDVVHVKSLATLVLIDQSETDW

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	0.80 RPM
SRP014902_testis	0.00 RPM	7.21 RPM
SRP018288_heart	0.00 RPM	10.14 RPM
SRP018288_kidney	0.00 RPM	15.47 RPM
SRP018288_liver	0.00 RPM	20.47 RPM
SRP018288_lung	0.00 RPM	2.14 RPM
SRP018856_adipose	0.00 RPM	5.91 RPM
SRP035408_brain	0.06 RPM	13.66 RPM
SRP035408_liver	0.00 RPM	44.33 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_557 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_557 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010887	1 retrocopy	retro_cfam_405,
Choloepus hoffmanni	ENSCHOG00000008731	3 retrocopies	retro_chof_1052, retro_chof_430, retro_chof_769,
Echinops telfairi	ENSETEG00000014816	1 retrocopy	retro_etel_1959,
Macaca mulatta	ENSMMUG00000017004	1 retrocopy	retro_mmul_1278,
Monodelphis domestica	ENSMODG00000020635	5 retrocopies	retro_mdom_638, retro_mdom_795, retro_mdom_945, retro_mdom_946, retro_mdom_947,
Oryctolagus cuniculus	ENSOCUG00000005941	2 retrocopies	retro_ocun_1338, retro_ocun_1470,
Ochotona princeps	ENSOPRG00000007086	1 retrocopy	retro_opri_847,
Sus scrofa	ENSSSCG00000022365	1 retrocopy	retro_sscr_557 ,
Tursiops truncatus	ENSTTRG00000003141	2 retrocopies	retro_ttru_1307, retro_ttru_606,