RetrogeneDB ID: retro_sscr_821

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:58029463..58029843(-)
• Located in intron of: ENSSSCG00000000591

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM5
• Ensembl ID: ENSSSCG00000026764
• Aliases: None
• Description: phosphoglycerate mutase family member 5 [Source:HGNC Symbol;Acc:28763]

Sequence

>retro_sscr_821
AAAGAGATTTTGCAATCTGGAGGAGAAAAACCCCGGCGCTCAGGCAGGACCACTACAAAGTCAAGGTCACGTACCTGGCA
TATCTCCCGCATAAGCTACTCCCAGTACCAGGCAGACGCCTCCCTGGAAAAGAACCGCGCTCTGATGCCCCTGAGTCGTG
AACCGGAAGAACTAACTGGTAACTGACCTACGGTAAGCTTGGGGCGGAACTTTAAATAAAATCCTCCATTGCTCTGAGAC
CCGCGCTATAGAAAAGTCCTACAGCAACAGCCAACACCTGCAAGGCGTCAGCAAATTTAGCACAGACCTGCTGGGGGAAA
GCGCCCCGTTTACAGGCTGACCCGCAAGGGTCTGCCCTGGAAGCCGCGGCTTTGCAGTAT

Alignment

ORF - retro_sscr_821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.77 %
• Parental protein coverage: 53.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  REPLSEPGEEELAS-RLDHY-KAKA-TRHIFLIRHSQYHVDASLEKDRTLTPLGREQAELTGL-RLASLG
          .E.L...GE....S.R.DHY.K....T.HI..I..SQY..DASLEK.R.L.PL.RE..ELTG.....SLG
Retrocopy KEILQSGGEKPRRS<RQDHY>KSRSRTWHISRISYSQYQADASLEKNRALMPLSREPEELTGN*PTVSLG

Parental  LKF-NKIVHSSMTRAIETTDIISKHLPGVCRVSTDLLREGAP-IEPDPPVWAGSPSAVQY
          ..F.NKI.H.S.TRAIE.....S.HL.GV...STDLL.E.AP....DP...A....A.QY
Retrocopy RNF>NKILHCSETRAIEKSYSNSQHLQGVSKFSTDLLGESAP>LQADPQGSALEAAALQY

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	24.69 RPM
SRP014902_testis	0.00 RPM	28.57 RPM
SRP018288_heart	0.00 RPM	17.34 RPM
SRP018288_kidney	0.00 RPM	15.27 RPM
SRP018288_liver	0.00 RPM	6.24 RPM
SRP018288_lung	0.00 RPM	20.26 RPM
SRP018856_adipose	0.00 RPM	17.68 RPM
SRP035408_brain	0.00 RPM	9.69 RPM
SRP035408_liver	0.00 RPM	6.96 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_821 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_821 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
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821 ,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,