RetrogeneDB ID: retro_sscr_866

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:47307658..47308047(-)
• Located in intron of: ENSSSCG00000003090

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR4
• Ensembl ID: ENSSSCG00000012784
• Aliases: None
• Description: signal sequence receptor, delta [Source:HGNC Symbol;Acc:11326]

Sequence

>retro_sscr_866
TCCCGCTGCTCGGTAGAGGCCCGTGTAGGGGCCCAGGTCGCCCCTTCCTACTATCCACCTCCAATGCCGCCACTTCTACC
GAGCCCGGCTTCACCGTGGCGCTCTCCCTGACGCTGGAGAACAGGATCCAGAACACGGCTCTCTGTGCTGACCTCAGTGG
AAAACAATGTCCTGTCACTCAGGGCCAGGACATGGGCGCTACCAGGTGCCCTGGAGCCCAGACCACGCGGGCACCTACAA
GGTCAAATTCTTTGACGAGGAGTCCTGCAGCCTCCCGAGGGAGGCGCAGACAAATACTGAGGACACTACCATCGTCCCAC
CTCTGTTCGGTCAGCGTGGACCATCGGGGCACTTGGCGTGGGCCCCGCGTCTCCACCGAGGTACCGGCT

Alignment

ORF - retro_sscr_866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.77 %
• Parental protein coverage: 82.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SCCSAEACVEPQITPSYY-TTSDAVISTETVFIVELSVTCKNRVQNMALYADVSGKQFPVTRGQDVG-RY
          S.CS.EA.V..Q..PSYY..TS.A..STE..F.V.LS.T..NR.QN.AL.AD.SGKQ.PVT.GQD.G.RY
Retrocopy SRCSVEARVGAQVAPSYY<STSNAATSTEPGFTVALSLTLENRIQNTALCADLSGKQCPVTQGQDMG<RY

Parental  QVSWSLDHKSAHAGTYEVRFFDEESYSLLRKAQRNNEDVSVIPP-LFTVSVDHRGTWNGPWVSTEVLA
          QV.WS.D....HAGTY.V.FFDEES.SL.R.AQ.N.ED...I.P.L..VSVDHRGTW.GP.VSTEV.A
Retrocopy QVPWSPD----HAGTYKVKFFDEESCSLPREAQTNTEDTT-IVP>LCSVSVDHRGTWRGPRVSTEVPA

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	104.46 RPM
SRP014902_testis	0.00 RPM	251.77 RPM
SRP018288_heart	0.08 RPM	33.66 RPM
SRP018288_kidney	0.10 RPM	70.73 RPM
SRP018288_liver	0.00 RPM	107.94 RPM
SRP018288_lung	0.10 RPM	160.38 RPM
SRP018856_adipose	0.00 RPM	78.46 RPM
SRP035408_brain	0.00 RPM	36.43 RPM
SRP035408_liver	0.00 RPM	98.28 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_866 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_866 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_866 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011328	1 retrocopy	retro_acar_97,
Callithrix jacchus	ENSCJAG00000011167	1 retrocopy	retro_cjac_2056,
Dasypus novemcinctus	ENSDNOG00000025714	2 retrocopies	retro_dnov_1204, retro_dnov_922,
Homo sapiens	ENSG00000180879	1 retrocopy	retro_hsap_2536,
Gorilla gorilla	ENSGGOG00000024329	1 retrocopy	retro_ggor_1585,
Loxodonta africana	ENSLAFG00000006908	1 retrocopy	retro_lafr_337,
Mustela putorius furo	ENSMPUG00000008803	1 retrocopy	retro_mputfur_148,
Nomascus leucogenys	ENSNLEG00000013602	1 retrocopy	retro_nleu_2738,
Otolemur garnettii	ENSOGAG00000006738	1 retrocopy	retro_ogar_691,
Procavia capensis	ENSPCAG00000009037	1 retrocopy	retro_pcap_139,
Sus scrofa	ENSSSCG00000012784	1 retrocopy	retro_sscr_866 ,