RetrogeneDB ID: retro_ptro_296

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:48689132..48689961(-)
• Located in intron of: ENSPTRG00000000718

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R8
• Ensembl ID: ENSPTRG00000000417
• Aliases: None
• Description: None

Sequence

>retro_ptro_296
ATGGTGGCAGTCACAAACTCTGGCTCCAGCCTCCCGCTGCTCCACTGCCCAACCTGGGCAGGTAAGCCCCCTCCTGGTTG
ACATCTGGATTTAGTTAAACAAGACAAACTAATTGAGAAACTGATTATTGGTGAAAAGAAGTATTACTTATTTGGGATAA
ACCTTGATTTGTGTGACTTTACCACTGAACACCAGTCTTGCTCTTGGATCCATACTGCACTTGTCTACCACAAGCATCTG
AGGAGAGTTTTCCTGATAGATCTCAACAGTACACACAGCACTTTCTTGGTCACATTCAGTTGGAGCCTCACAAGCCTCAG
CAAATTCCGATTGATTCCAGGGTCTCATTTGACACATCCACAGGGGCATACACTTTGCGCGAGATACTTGGGCCATTGCC
ATTGGCTCTGAAAGGAGTTGAGAAGACGGGTGAAGAGGATGATTAACTCAGGGGCTTACTGGGGCTTCCAGAGGAGGAAA
CTAAGCTTGATAACCTGACATAGTTCAACACTGCCCACAACAAGTGGATTTCCACCTTTACCATTGAGGAGGGAAATCTA
ACATTCCAAGACCAAAGAGGAAGAGGAAGAACTCCCGGGTGACATTCAGTGAGGATGATGAGATCATCAACTCAGAGAAT
GTGGATCCCTCAGTTTGTCGATTCAGGAACATAGTGCAAACTGCAGTGGTCCCAGTCAAGAAGAAGCTGGGGGAGGGCCC
TGGCTCCTTGGGCCTGGAGGAATCAGGGAGAAGGCGCATGCAGAACTTTGCCTTCAGGGGAGGACTCTACGGGGGCCTGT
GCCCTACTCACAGTGAAGCAGGCTCCCAG

Alignment

ORF - retro_ptro_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.72 %
• Parental protein coverage: 78.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAANSGSSLPLFDCPTWAGKPPPGLHLDVVKGDKLIEKLIIDEKKYYLFGRNPDLCDFTIDHQSCSRV
          M.A..NSGSSLPL..CPTWAGKPPPG.HLD.VK.DKLIEKLII.EKKYYLFG.N.DLCDFT..HQSCS..
Retrocopy MVAVTNSGSSLPLLHCPTWAGKPPPG*HLDLVKQDKLIEKLIIGEKKYYLFGINLDLCDFTTEHQSCSWI

Parental  HAALVYHKHLKRVFLIDLNSTHGT-FLGHIRLEPHKPQQIPIDSTVSFGASTRAYTLREKPQTLPSAVKG
          H.ALVYHKHL.RVFLIDLNSTH.T.FLGHI.LEPHKPQQIPIDS.VSF..ST.AYTLRE....LP.A.KG
Retrocopy HTALVYHKHLRRVFLIDLNSTHST<FLGHIQLEPHKPQQIPIDSRVSFDTSTGAYTLREILGPLPLALKG

Parental  DEKMGGEDDELKGLLGLPEEETELDNLTEFNTAHNKRISTLTIEEGNL-DIQRPKRKRKNSRVTFSEDDE
          .EK.G.EDD.L.GLLGLPEEET.LDNLT.FNTAHNK.IST.TIEEGNL..I.RPKRKRKNSRVTFSEDDE
Retrocopy VEKTGEEDD*LRGLLGLPEEETKLDNLT*FNTAHNKWISTFTIEEGNL<NIPRPKRKRKNSRVTFSEDDE

Parental  IINPEDVDPSVGRFRNMVQTAVVPVKKKRVEGPGSLGLEESGSRRMQNFAFSGGLYGGLPPTHSEAGSQ
          IIN.E.VDPSV.RFRN.VQTAVVPVKKK..EGPGSLGLEESG.RRMQNFAF.GGLYGGL.PTHSEAGSQ
Retrocopy IINSENVDPSVCRFRNIVQTAVVPVKKKLGEGPGSLGLEESGRRRMQNFAFRGGLYGGLCPTHSEAGSQ

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
SRP007412_brain_prefrontal_cortex	0.20 RPM	19.45 RPM
SRP007412_cerebellum	0.04 RPM	31.58 RPM
SRP007412_heart	0.09 RPM	13.17 RPM
SRP007412_kidney	0.08 RPM	22.78 RPM
SRP007412_liver	0.00 RPM	18.53 RPM
SRP007412_testis	0.21 RPM	55.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_296 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_296 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_380
Macaca mulatta	retro_mmul_491

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012023	1 retrocopy	retro_cfam_334,
Homo sapiens	ENSG00000117751	1 retrocopy	retro_hsap_380,
Gorilla gorilla	ENSGGOG00000012062	1 retrocopy	retro_ggor_387,
Loxodonta africana	ENSLAFG00000017834	1 retrocopy	retro_lafr_1173,
Macaca mulatta	ENSMMUG00000006933	1 retrocopy	retro_mmul_491,
Pan troglodytes	ENSPTRG00000000417	1 retrocopy	retro_ptro_296 ,
Ictidomys tridecemlineatus	ENSSTOG00000004381	2 retrocopies	retro_itri_1611, retro_itri_1704,