RetrogeneDB ID: retro_sscr_388

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:150069261..150069829(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI2
• Ensembl ID: ENSSSCG00000010876
• Aliases: DESI2, DeSI-2, FAM152A, PNAS-4, PPPDE1
• Description: Sus scrofa PPPDE peptidase domain containing 1 (PPPDE1), mRNA. [Source:RefSeq mRNA;Acc:NM_001097419]

Sequence

>retro_sscr_388
ATGGGGGCTAACCAATTAGTCGTGCTCAACGTGTAGACTCGTACTGGATGAATGAACACACCTCATCCATCGGAATTGGA
GTTTTTCATTCAGAAATTGAAATATGTGGCAGAGAATTTGCTTATTCCCCTTTTCTGGAATATTTGAAATTCCCCCCAGG
ACATGCTTCTGAACTAGGAGAAGCATTTAAATTTAAATAAGCTGTTGTTTGGGGGAGCAATAACTTCCTAGAAGATGATA
TAGAAAAAATTGTAGAAGAATTGGGAAAAGAATACAAAGGCAATGACTATCATTTGATGCATAAAAATGCAATCATTTTT
CTTCGGCTTTATCAGTGATTCTTTGTGGGAAAGAGATTCCTCGCTGGATCAATCCACTCGCCTACTTCAGCTCCTGCATA
CCCTTTCTCCAGAGATGCCTCCCAAAGGAGTGGCTCACTCCCGCAGTCCTGCAGTCTAGAGTCAGCAAGGAGCTCCAGGG
AGAACTGGAGGAGGTAGAGGATACAGCAGCCTCCACCTCCATGGGTAGCACTGCAGCAGGCTCCAGGCCCGGGCACCACA
TCAAACTC

Alignment

ORF - retro_sscr_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGANQLVVLNV-YDMYWMNEYTSSIGIGVFHSGIEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKF
          MGANQLVVLNV..D.YWMNE.TSSIGIGVFHS.IE..GREFAY.....PF.......PG.ASELGE.FKF
Retrocopy MGANQLVVLNV<VDSYWMNEHTSSIGIGVFHSEIEICGREFAYS----PFLEYLKFPPGHASELGEAFKF

Parental  KEAVVLGSTDFLEDDIEKIVEELGKEYKGNAYHLMHKN-CNHFSSALSEILCGKEIPRWINRLAYFSSCI
          K.AVV.GS..FLEDDIEKIVEELGKEYKGN.YHLMHKN.CNHFSSALS.ILCGKEIPRWIN.LAYFSSCI
Retrocopy K*AVVWGSNNFLEDDIEKIVEELGKEYKGNDYHLMHKN<CNHFSSALSVILCGKEIPRWINPLAYFSSCI

Parental  PFLQSCLPKEWLTPAALQSSVSQELQDELEEAEDAAASASMGSASAGSRPGRHTKL
          PFLQ.CLPKEWLTPA.LQS.VS.ELQ.ELEE.ED.AAS.SMGS..AGSRPG.H.KL
Retrocopy PFLQRCLPKEWLTPAVLQSRVSKELQGELEEVEDTAASTSMGSTAAGSRPGHHIKL

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	82.03 RPM
SRP014902_testis	0.00 RPM	52.62 RPM
SRP018288_heart	0.00 RPM	27.61 RPM
SRP018288_kidney	0.00 RPM	31.32 RPM
SRP018288_liver	0.00 RPM	29.74 RPM
SRP018288_lung	0.00 RPM	80.14 RPM
SRP018856_adipose	0.00 RPM	20.64 RPM
SRP035408_brain	0.00 RPM	17.47 RPM
SRP035408_liver	0.06 RPM	17.09 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_388 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_388 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000016	1 retrocopy	retro_chof_2439,
Dasypus novemcinctus	ENSDNOG00000003484	3 retrocopies	retro_dnov_1042, retro_dnov_2533, retro_dnov_539,
Erinaceus europaeus	ENSEEUG00000009507	2 retrocopies	retro_eeur_394, retro_eeur_470,
Homo sapiens	ENSG00000121644	1 retrocopy	retro_hsap_2071,
Gorilla gorilla	ENSGGOG00000009797	1 retrocopy	retro_ggor_1493,
Nomascus leucogenys	ENSNLEG00000004019	1 retrocopy	retro_nleu_2734,
Ochotona princeps	ENSOPRG00000015368	2 retrocopies	retro_opri_1007, retro_opri_963,
Pongo abelii	ENSPPYG00000000055	1 retrocopy	retro_pabe_1685,
Pan troglodytes	ENSPTRG00000002180	1 retrocopy	retro_ptro_1384,
Sus scrofa	ENSSSCG00000010876	1 retrocopy	retro_sscr_388 ,
Drosophila melanogaster	FBgn0033551	1 retrocopy	retro_dmel_30,