RetrogeneDB ID: retro_sscr_623

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:64735427..64735961(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLA2G12A
• Ensembl ID: ENSSSCG00000009139
• Aliases: None
• Description: phospholipase A2, group XIIA [Source:HGNC Symbol;Acc:18554]

Sequence

>retro_sscr_623
CCCCCGTGGCCCATGTTGGCACTCCTCCTGGACTGCAGCTTTCAGTTGCCGGGAGCAAGCCCAGACCACCTACTGGAGGG
CCACCCTGTAGACTAACCAGAGCAGCAGTCAGAAGATAAACACATACCTGAACTCCGTTTTAGACCTCTTGGCAGGTCAG
GACCGGCTCTGCTAGTATCAATGCAGTGATGGATCTAAGCCTTTCCCTCGTGATTATATACCCTCCCTGCCTAAGAGATG
TGGTTTTTCACTCTTTGATGTTCACGGGAACAATGGCATCCCTTCCCTGACAAAGTGCTTCAGCTAAGCAACGGGTACTA
TGAGACCTGTGGCAAAAGCAACAAGGACTGGGATGAGGAGTTCCAGTGTTGTCCCTCCAAGATCTGCCGAGATGGGCACA
AAACACTAACACCAGCTCAGTGTGTTCAGGCACTTGAAACCACAGTGCAAGTCTTGTCTGACAGTGTTAGACAGTTAGCC
TGAAAATCATACCTGAACAGCCAACGAGCTGCCCATAGGTGTCGCTGGGAAGAA

Alignment

ORF - retro_sscr_623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.33 %
• Parental protein coverage: 94.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PALALLLLLL-TAAFRCQEQAQPTDWRATLKTIRNGVHKIDTYLNAALDLLGGEDGLCQYKCNDGSKPFP
          P....L.LLL.TAAF.C.EQAQ.T.WRATL.T......KI.TYLN..LDLL.G.D.LC.Y.C.DGSKPFP
Retrocopy PPWPMLALLL>TAAFSCREQAQTTYWRATL*TNQSSSQKINTYLNSVLDLLAGQDRLC*YQCSDGSKPFP

Parental  RYGYKPSPPNGCGSPLFGVHLNIGIPSLT-KCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRDVQKTLG
          R..Y.PS.P..CG..LF.VH.N.GIPSLT.K........YETCGKS..D.DEEFQ.C.SKICRD..KTL.
Retrocopy R-DYIPSLPKRCGFSLFDVHGNNGIPSLT<KVLQLSNGYYETCGKSNKDWDEEFQCCPSKICRDGHKTLT

Parental  LAQHIQACETTVELLFDSVIHLGCKPYLDSQRAACRCRYQE
          .AQ..QA.ETTV..L.DSV..L..K.YL.SQRAA.RCR..E
Retrocopy PAQCVQALETTVQVLSDSVRQLA*KSYLNSQRAAHRCRWEE

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	44.73 RPM
SRP014902_testis	0.00 RPM	38.33 RPM
SRP018288_heart	0.08 RPM	36.57 RPM
SRP018288_kidney	0.20 RPM	25.32 RPM
SRP018288_liver	0.00 RPM	28.30 RPM
SRP018288_lung	0.00 RPM	25.66 RPM
SRP018856_adipose	0.06 RPM	20.77 RPM
SRP035408_brain	0.13 RPM	25.92 RPM
SRP035408_liver	0.00 RPM	27.24 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_623 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_623 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_623 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623 , retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,