RetrogeneDB ID: retro_sscr_1087

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL893245.2:64218..64567(+)
• Located in intron of: ENSSSCG00000028318

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14B
• Ensembl ID: ENSSSCG00000013035
• Aliases: PHI-1, PPP1R14B, pPHI-1
• Description: Sus scrofa ubiquitous PKC-potentiated PP1 inhibitor (PHI-1), mRNA. [Source:RefSeq mRNA;Acc:NM_214115]

Sequence

>retro_sscr_1087
CCTAGGCATCTACTTTCAGATCCCCTGGGGTTGCAAGCAGAGCTAGGTGACACAGATGACGAGAGCCCAGTGAGGTGCCA
AAGGAAGGTCACGGTCAAGTAAGACCACCAGGAGCCATAGAAGGGCCTCAGCCTAGAGGAGTGGGTCCTAGAGCAGCTAC
TTTCCCCTACGACTGCCAGGAAGAGGAAAAGCCAGAGTTGGAGACTGCCGTGGCTGAACTCCTGGACATGAAGAGCAGTG
ATACCCAGGCTGCCAGGGTCAAGGATCTGCTGGTCGACTGTTACAAACCCACTGATGCTCTCACCTCTGGCCTGCTGGAC
AAGATCCAGGGATGCAGTAGCTGAGCACA

Alignment

ORF - retro_sscr_1087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.83 %
• Parental protein coverage: 80.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PRVYFQSPPGAAGEGPGGADDEGPVRRQGKVTVKYDRKELRKRLNLEEWILEQL-TRLYDCQEEEIPELE
          PR.....P.G...E..G..DDE.PVR.Q.KVTVK.D..E..K.L.LEEW.LEQL.T..YDCQEEE.PELE
Retrocopy PRHLLSDPLGLQAE-LGDTDDESPVRCQRKVTVK*DHQEP*KGLSLEEWVLEQL<TFPYDCQEEEKPELE

Parental  IDVDELLDMESDDTRAARVKELLVDCYKPTEAFISGLLDKIR-GMQKLST
          ..V.ELLDM.S.DT.AARVK.LLVDCYKPT.A..SGLLDKI..GMQ.LST
Retrocopy TAVAELLDMKSSDTQAARVKDLLVDCYKPTDALTSGLLDKIQ<GMQ*LST

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	95.30 RPM
SRP014902_testis	0.28 RPM	47.24 RPM
SRP018288_heart	0.03 RPM	11.89 RPM
SRP018288_kidney	0.00 RPM	19.70 RPM
SRP018288_liver	0.00 RPM	18.87 RPM
SRP018288_lung	0.00 RPM	20.67 RPM
SRP018856_adipose	0.00 RPM	85.25 RPM
SRP035408_brain	0.00 RPM	20.90 RPM
SRP035408_liver	0.00 RPM	17.47 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1087 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1087 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018111	3 retrocopies	retro_cjac_3591, retro_cjac_428, retro_cjac_532,
Homo sapiens	ENSG00000173457	4 retrocopies	retro_hsap_2205, retro_hsap_3101, retro_hsap_3655, retro_hsap_3838,
Mustela putorius furo	ENSMPUG00000013208	2 retrocopies	retro_mputfur_235, retro_mputfur_798,
Nomascus leucogenys	ENSNLEG00000004890	2 retrocopies	retro_nleu_324, retro_nleu_335,
Pan troglodytes	ENSPTRG00000041138	6 retrocopies	retro_ptro_1674, retro_ptro_2097, retro_ptro_2480, retro_ptro_2614, retro_ptro_3089, retro_ptro_935,
Sus scrofa	ENSSSCG00000013035	2 retrocopies	retro_sscr_1087 , retro_sscr_892,
Ictidomys tridecemlineatus	ENSSTOG00000021959	1 retrocopy	retro_itri_1110,