RetrogeneDB ID: retro_sscr_750

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:19917157..19917389(+)
• Located in intron of: ENSSSCG00000005997

Retrocopy information

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

Parental gene information

• Parental gene symbol: BOLA3
• Ensembl ID: ENSSSCG00000008291
• Aliases: None
• Description: bolA homolog 3 (E. coli) [Source:HGNC Symbol;Acc:24415]

Sequence

>retro_sscr_750
ATGGCAACCTGGAGCCTGGCCACCACAGTCCCTGTGCTCCACGGGGACTTGAGGGCTTCCTCTTCTCCACTGTGCCTGGT
GGATGTTTGCCTTGCAGGCTGAGGGGGAGCTCAAAGAGACCCAGATTCTTAAAAGAAAAATTTCCTCAAGCTACAGCTAA
CAAAGTCACTGACATTTCAGGAGGCTGTGGGCAATGTATGAAATTCCAATCAAACTGGAAGAATTTATGGAT

Alignment

ORF - retro_sscr_750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 70.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAWSPAAAAPLLRGSR-GLPLLHSAQRMFASQTEGERKVTQILK-EKFPRATAIKVTDISGGCG-AMYE
          MA.WS.A...P.L.G...GLPLLH.A..MFA.Q.EGE.K.TQILK.EKFP.ATA.KVTDISGGCG.AMYE
Retrocopy MATWSLATTVPVLHGDL>GLPLLHCAWWMFALQAEGELKETQILK>EKFPQATANKVTDISGGCG<AMYE

Parental  IQIESEEFKE
          I.I..EEF..
Retrocopy IPIKLEEFMD

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	39.55 RPM
SRP014902_testis	0.00 RPM	20.37 RPM
SRP018288_heart	0.00 RPM	51.37 RPM
SRP018288_kidney	0.00 RPM	64.13 RPM
SRP018288_liver	0.00 RPM	32.94 RPM
SRP018288_lung	0.00 RPM	32.18 RPM
SRP018856_adipose	0.00 RPM	44.39 RPM
SRP035408_brain	0.00 RPM	44.94 RPM
SRP035408_liver	0.00 RPM	37.37 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_750 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_750 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_750 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008739	1 retrocopy	retro_cfam_1574,
Callithrix jacchus	ENSCJAG00000017844	1 retrocopy	retro_cjac_1112,
Dasypus novemcinctus	ENSDNOG00000008309	2 retrocopies	retro_dnov_2474, retro_dnov_510,
Myotis lucifugus	ENSMLUG00000016364	1 retrocopy	retro_mluc_1407,
Mustela putorius furo	ENSMPUG00000007813	1 retrocopy	retro_mputfur_1519,
Mus musculus	ENSMUSG00000045160	1 retrocopy	retro_mmus_1648,
Oryctolagus cuniculus	ENSOCUG00000016658	1 retrocopy	retro_ocun_51,
Otolemur garnettii	ENSOGAG00000003502	1 retrocopy	retro_ogar_1839,
Sorex araneus	ENSSARG00000001754	1 retrocopy	retro_sara_83,
Sus scrofa	ENSSSCG00000008291	1 retrocopy	retro_sscr_750 ,
Tursiops truncatus	ENSTTRG00000006698	3 retrocopies	retro_ttru_1149, retro_ttru_1493, retro_ttru_254,