RetrogeneDB ID: retro_sscr_488

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:10600006..10600323(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR83OS
• Ensembl ID: ENSSSCG00000013721
• Aliases: None
• Description: WD repeat domain 83 opposite strand [Source:HGNC Symbol;Acc:30203]

Sequence

>retro_sscr_488
ATGTCCATGAACAATATGTTGGACCCACAGAGCCCAACAAAGTGCTGAGGTACAAGGCCCCGCCGAGCGAGTGTAACCCA
GTATTGGATGACCTAACACTGGAGTACATGAAACTGCTTGCCATGATCTTAAGCGTGTGTGGCCTCATGCTCAAGCCACA
GTGGTGCACTTGGGTTGCTGTCTACTGCTTCTTCATTAGCTTTGCCAACTCCCAGAGCCCTAAGGACACTAAGCAGATGA
TGAGTAGCTTCCTGCTGCCCATCTCTGCTTGATAGGTAATGTCCTATCTGCAGAACCCTCAGCCCATGATGCCCCCC

Alignment

ORF - retro_sscr_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.77 %
• Parental protein coverage: 99.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSANSMSDPR-RPNKVLRYKPPPSECNPALDDPTPDYMNLLGMIFSMCGLMLKLKWCAWVAVYCSFISFA
          MS.N.M.DP...PNKVLRYK.PPSECNP.LDD.T..YM.LL.MI.S.CGLMLK..WC.WVAVYC.FISFA
Retrocopy MSMNNMLDPQ<EPNKVLRYKAPPSECNPVLDDLTLEYMKLLAMILSVCGLMLKPQWCTWVAVYCFFISFA

Parental  NSRSSEDTKQMMSSFMLSISA-VVMSYLQNPQPMTPP
          NS.S..DTKQMMSSF.L.ISA..VMSYLQNPQPM.PP
Retrocopy NSQSPKDTKQMMSSFLLPISA**VMSYLQNPQPMMPP

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	73.80 RPM
SRP014902_testis	0.00 RPM	68.60 RPM
SRP018288_heart	0.00 RPM	31.75 RPM
SRP018288_kidney	0.00 RPM	52.01 RPM
SRP018288_liver	0.00 RPM	43.50 RPM
SRP018288_lung	0.00 RPM	52.24 RPM
SRP018856_adipose	0.00 RPM	70.25 RPM
SRP035408_brain	0.03 RPM	9.46 RPM
SRP035408_liver	0.00 RPM	10.69 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_488 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028908	2 retrocopies	retro_cfam_1489, retro_cfam_1951,
Callithrix jacchus	ENSCJAG00000005285	1 retrocopy	retro_cjac_133,
Echinops telfairi	ENSETEG00000019481	1 retrocopy	retro_etel_1133,
Felis catus	ENSFCAG00000000463	1 retrocopy	retro_fcat_1902,
Macropus eugenii	ENSMEUG00000014450	3 retrocopies	retro_meug_1695, retro_meug_1733, retro_meug_2081,
Mus musculus	ENSMUSG00000059355	2 retrocopies	retro_mmus_1327, retro_mmus_2061,
Pteropus vampyrus	ENSPVAG00000013403	1 retrocopy	retro_pvam_1464,
Sus scrofa	ENSSSCG00000013721	1 retrocopy	retro_sscr_488 ,
Tupaia belangeri	ENSTBEG00000001250	1 retrocopy	retro_tbel_2034,