RetrogeneDB ID: retro_sscr_524

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:40694994..40695293(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSSSCG00000022190
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 variant 2 [Source:HGNC Symbol;Acc:12495]

Sequence

>retro_sscr_524
AATGGTCCAGTTAGCTGGGGCCTTGAGCTGAGGAATAAATGATGCTTCCAAAGTAGGCAGCTATCATTATTAGGTCACAG
AGACAACTTATGAAAACAGAATATACAGACTGAAATTATAGTGTGTACCTAAATATTCAGAAGCTTCTCCATTGGTTATT
TTGCAACAAAATATATGAATGAAATAAATAATTCCAGTGAAATGGTAGAGGCATTGAACATAGTGGGGTTAACAAAACGG
CAAAATTCATAAAAGTTAAAAATTGTACTTCAGAGTTAAGATATGTAATACTGCTCAAA

Alignment

ORF - retro_sscr_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.77 %
• Parental protein coverage: 70.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DGTVSWGLE-DDEDMTLTRWTGMIIGPPR-TNYENRIYSLKIECGPKYPEAPPSV-RFVTKINMNGINNS
          .G.VSWGLE...E.M.L......II...R.T.YENRIY.LK..C.PKY.EA.P.V..F.TK..MN.INNS
Retrocopy NGPVSWGLE<AEE*MMLPK*AAIIIRSQR<TTYENRIYRLKL*CVPKYSEASPLV<YFATKY-MNEINNS

Parental  SGMVDARSIPVLAKWQNSYSIKVVLQ-ELRRLMMSK
          S.MV.A..I..L.K.QNS...K.VLQ.ELR.....K
Retrocopy SEMVEALNIVGLTKRQNS*KLKIVLQ<ELRYVILLK

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	15.13 RPM
SRP014902_testis	0.00 RPM	25.32 RPM
SRP018288_heart	0.00 RPM	25.12 RPM
SRP018288_kidney	0.00 RPM	44.33 RPM
SRP018288_liver	0.00 RPM	29.58 RPM
SRP018288_lung	0.00 RPM	55.80 RPM
SRP018856_adipose	0.00 RPM	37.17 RPM
SRP035408_brain	0.00 RPM	130.28 RPM
SRP035408_liver	0.00 RPM	27.42 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_524 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_524 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_524 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2739
Bos taurus	retro_btau_902

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032182	1 retrocopy	retro_cjac_814,
Loxodonta africana	ENSLAFG00000017749	1 retrocopy	retro_lafr_1168,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Mus musculus	ENSMUSG00000022674	4 retrocopies	retro_mmus_1385, retro_mmus_189, retro_mmus_2048, retro_mmus_2770,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Procavia capensis	ENSPCAG00000000293	1 retrocopy	retro_pcap_138,
Sus scrofa	ENSSSCG00000022190	1 retrocopy	retro_sscr_524 ,
Sus scrofa	ENSSSCG00000030632	1 retrocopy	retro_sscr_431,
Tursiops truncatus	ENSTTRG00000008325	1 retrocopy	retro_ttru_1623,