RetrogeneDB ID: retro_sscr_236

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:78877715..78878362(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTEN
• Ensembl ID: ENSSSCG00000010440
• Aliases: None
• Description: phosphatase and tensin homolog [Source:HGNC Symbol;Acc:9588]

Sequence

>retro_sscr_236
ATGATAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGAATGGATTTGACTTAGACTTGACCTA
TATTTATCCAAATATTATTGCTCTGGGGTTTCCTGCAGAAAGACTTTAAGGCATATACAGGAACAATATTGATGATGTAG
TAAGGATTTTGGATTCAAAGCATAAAAACCATTACAAGATATACAATCTATGTGCTGAAAGACATTATGATACCGCCACA
TTTAACTGCAGAGTTGCACAGTATCCTTTTGAAGATCATAATCCACCACAGCTAGAATTTATCAAACCTTTTTGTGAAGA
TCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAACCTGGAAAAGGATGAACTGGTGTAA
TGATTTGTGCATATTTGTTTCATCCGGGCAAATTTTTAAAGGCACAAGATTTCTATGGGGAAGTAAGGACCAGAGACAAA
AAGGGAGTAACTCTTCCCAGTCAGAGTCACTATGTGTATTATTACAGCTACCTGTTAAAGAATCATCTGGATTATAGACC
AGTGCACTGTTGTTTCGCAAGATGTTGTTTGAAACTATTCCAGTGTTCAGTGGTGGAACATGCAATCCTCAGTTTGTGGT
CTGCCAG

Alignment

ORF - retro_sscr_236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 54.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNL
          M.AIIKEIVSRNKRRYQE.GFDLDLTYIYPNIIA.GFPAERL.G.YRNNIDDVVR.LDSKHKNHYKIYNL
Retrocopy MIAIIKEIVSRNKRRYQENGFDLDLTYIYPNIIALGFPAERL*GIYRNNIDDVVRILDSKHKNHYKIYNL

Parental  CAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICAYLL
          CAERHYDTA.FNCRVAQYPFEDHNPPQLE.IKPFCEDLDQWLSEDDNHVAAIHCK.GKG.TGVMICAYL.
Retrocopy CAERHYDTATFNCRVAQYPFEDHNPPQLEFIKPFCEDLDQWLSEDDNHVAAIHCKPGKG*TGVMICAYLF

Parental  HRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPV-ALLFHKMMFETIPMFSGG
          H.GKFLKAQ...DFYGEVRTRDKKGVT.PSQ..YVYYYSYLLKNHLDYRPV.ALLF.KM.FETIP.FSGG
Retrocopy HPGKFLKAQ---DFYGEVRTRDKKGVTLPSQSHYVYYYSYLLKNHLDYRPV<ALLFRKMLFETIPVFSGG

Parental  TCNPQFVVCQ
          TCNPQFVVCQ
Retrocopy TCNPQFVVCQ

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	13.01 RPM
SRP014902_testis	0.00 RPM	24.75 RPM
SRP018288_heart	0.00 RPM	60.64 RPM
SRP018288_kidney	0.00 RPM	31.13 RPM
SRP018288_liver	0.00 RPM	36.30 RPM
SRP018288_lung	0.00 RPM	112.01 RPM
SRP018856_adipose	0.00 RPM	29.42 RPM
SRP035408_brain	0.00 RPM	6.99 RPM
SRP035408_liver	0.00 RPM	15.97 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_236 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_236 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009252	1 retrocopy	retro_chof_578,
Homo sapiens	ENSG00000171862	1 retrocopy	retro_hsap_4245,
Gorilla gorilla	ENSGGOG00000000893	1 retrocopy	retro_ggor_2846,
Nomascus leucogenys	ENSNLEG00000012141	1 retrocopy	retro_nleu_1280,
Pongo abelii	ENSPPYG00000002448	1 retrocopy	retro_pabe_3393,
Sarcophilus harrisii	ENSSHAG00000003709	1 retrocopy	retro_shar_828,
Sus scrofa	ENSSSCG00000010440	2 retrocopies	retro_sscr_236 , retro_sscr_237,