RetrogeneDB ID: retro_sscr_243

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:22268770..22269685(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP6C
• Ensembl ID: ENSSSCG00000005600
• Aliases: None
• Description: protein phosphatase 6, catalytic subunit [Source:HGNC Symbol;Acc:9323]

Sequence

>retro_sscr_243
ATGGCGCCCCTGGACTTGGACAAGTATGTGGAGATAGTGCGTCTATGCAAGTACCTGCCCGAGAACGACCTGAAGCGGTT
GTGTGACTATGTTTGTGACCTCCTCTTGGAAGAGTCAAATGTCCAGCCAGTGTCGACACCTGTAACAGTGTGTGGAGACA
TACACGGACAGTTTTATGATCTTTGTGAACTATTCAGAACTGGAGGTCAGGTTCCTGACACAAACTACATATTTATGGGT
GATTTTGTAGACAGAGGTTATTATAGTTTGGAGACCTTCACTTACCTTCTTGCACTAAAGGCTAAATGGCCTGATCGTAT
TACACTTTTGTGAGGAAATCATGAGAGTAGACAGATAACACAGGTGTATGGATTTTATGATGAGTGCCAAACCAAATATG
GAAATGCTAATGCCTGGAGATACTGTACCAAAGTTTTTGACATGCTCACAGTAGCAGCTTTAATAGATGAGCAGATTTTG
TGTGTTCATGGTGGTTTATCTCCTGATATCAAAACACTGGATCAGATCCGTACTATTGAACGGAATCAAGAAATTCCTCA
TAAAGGAGCATTTTGTGATCTGGTTTGGTCAGATCCTGAAGATGTGGATACTTGGGCAATCAGTCCCCGAGGAGCAGGTT
GACTTTTTGGCGCAAAGGTCACAAATGAGTTTGTTCATATCAACAACTTAAAACTCATCTGCAGAGCACACCAGCTAGTG
CATGAAGGCCATAAATTTATGTTTGATGAGAAGCTGGTAACAGTATGGTCTGCTCCTAATTACTGCTATCGTTGTGGAAA
TATTGCTTCGATCATGGTCTTCAAAGATGTAAATACAAGAGAACCAAAGTTATTCCGGGCAGTTCCAGATTCAGAACGTG
TTATTCCTCCCAGAACGACAATGCCGTATTTCCTT

Alignment

ORF - retro_sscr_243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPLDLDKYVEIARLCKYLPENDLKRLCDYVCDLLLEESNVQPVSTPVTVCGDIHGQFYDLCELFRTGGQ
          MAPLDLDKYVEI.RLCKYLPENDLKRLCDYVCDLLLEESNVQPVSTPVTVCGDIHGQFYDLCELFRTGGQ
Retrocopy MAPLDLDKYVEIVRLCKYLPENDLKRLCDYVCDLLLEESNVQPVSTPVTVCGDIHGQFYDLCELFRTGGQ

Parental  VPDTNYIFMGDFVDRGYYSLETFTYLLALKAKWPDRITLLRGNHESRQITQVYGFYDECQTKYGNANAWR
          VPDTNYIFMGDFVDRGYYSLETFTYLLALKAKWPDRITLL.GNHESRQITQVYGFYDECQTKYGNANAWR
Retrocopy VPDTNYIFMGDFVDRGYYSLETFTYLLALKAKWPDRITLL*GNHESRQITQVYGFYDECQTKYGNANAWR

Parental  YCTKVFDMLTVAALIDEQILCVHGGLSPDIKTLDQIRTIERNQEIPHKGAFCDLVWSDPEDVDTWAISPR
          YCTKVFDMLTVAALIDEQILCVHGGLSPDIKTLDQIRTIERNQEIPHKGAFCDLVWSDPEDVDTWAISPR
Retrocopy YCTKVFDMLTVAALIDEQILCVHGGLSPDIKTLDQIRTIERNQEIPHKGAFCDLVWSDPEDVDTWAISPR

Parental  GAGWLFGAKVTNEFVHINNLKLICRAHQLVHEGYKFMFDEKLVTVWSAPNYCYRCGNIASIMVFKDVNTR
          GAG.LFGAKVTNEFVHINNLKLICRAHQLVHEG.KFMFDEKLVTVWSAPNYCYRCGNIASIMVFKDVNTR
Retrocopy GAG*LFGAKVTNEFVHINNLKLICRAHQLVHEGHKFMFDEKLVTVWSAPNYCYRCGNIASIMVFKDVNTR

Parental  EPKLFRAVPDSERVIPPRTTTPYFL
          EPKLFRAVPDSERVIPPRTT.PYFL
Retrocopy EPKLFRAVPDSERVIPPRTTMPYFL

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	0.13 RPM	13.94 RPM
SRP014902_testis	0.28 RPM	11.74 RPM
SRP018288_heart	1.39 RPM	25.38 RPM
SRP018288_kidney	3.25 RPM	43.24 RPM
SRP018288_liver	1.76 RPM	24.47 RPM
SRP018288_lung	0.92 RPM	27.59 RPM
SRP018856_adipose	0.06 RPM	31.86 RPM
SRP035408_brain	1.05 RPM	23.03 RPM
SRP035408_liver	0.91 RPM	12.83 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_243 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_243 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012357	3 retrocopies	retro_chof_1759, retro_chof_183, retro_chof_608,
Dasypus novemcinctus	ENSDNOG00000015319	1 retrocopy	retro_dnov_1700,
Erinaceus europaeus	ENSEEUG00000010197	1 retrocopy	retro_eeur_706,
Macaca mulatta	ENSMMUG00000020549	1 retrocopy	retro_mmul_698,
Rattus norvegicus	ENSRNOG00000015145	1 retrocopy	retro_rnor_2074,
Sarcophilus harrisii	ENSSHAG00000008282	1 retrocopy	retro_shar_146,
Sus scrofa	ENSSSCG00000005600	1 retrocopy	retro_sscr_243 ,