RetrogeneDB ID: retro_ptro_2974

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL389636.1:9750..10523(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4R2
• Ensembl ID: ENSPTRG00000015108
• Aliases: None
• Description: None

Sequence

>retro_ptro_2974
GAGAAACAGATTCAGTGGTCCCAATTTAAAGGCTATTTTATTTTCAAACTGGAGAAAGTGATGGATGATTTCAGAACTTC
AGCTCCTGCGCCAAGAGGTCCTCCCAACCCTAATGTCGAATATATTCCCTTTGATGAAACAAAGGAAAGAATACTGAAAA
CGGTCACTGGATTTAACCGTATCCCTTTTACTATTCAGTGATTATGTGAATTGTTAACAGATCCAAGGAGAAACTATACA
GGAACAGACAAATTTCTCACAGGAGTAGAAAAGAACGTGATGGTTGTTAGCTGTGTTTATCCTTCTTCAGAGAAAAACAA
TTCCAATAGTTTAAATCGAATGAATGGTGTTATGTTTCCTGGAAATGCACCAAGCTATACTGAGAGGTCTAATATAAATG
GGCCTGGGACACCCAGGCCACTTAATCGACAAAGGTTTCTTTGTCAGCCCCCATGACAACAAATGGGTGGCCTGAGAGCA
CAGACAGCAAAGAGGCAAATTTGCAGCAAAATGAAGAGAAAACTCACAGTGACTCTTCGACATCTGAATCAGAAGTTTCC
TCAGTGAACCCTTTGAAAAATAAACATCCAGATGAAGATGCTGTGGAAGCTGAGGGGCATGAGGTAAAAAGACTCAGGTT
TGACAAAAAAGGCAAAGTTGGAGAAACAGCCAGTCAAGCGACTTGCAGCGAAATTTCTTCAGTTATGGTAGAAGAAACAG
AAGCATCACCTTCATCTCACGATAAAGAGAAAGAAAGCCGTGGTACCCGGCAG

Alignment

ORF - retro_ptro_2974 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.58 %
• Parental protein coverage: 61.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETMIQWSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCE
          E..IQWSQFKGYFIFKLEKVMDDFRTSAP.PRGPPNPNVEYIPFDE.KERILK.VTGFN.IPFTIQ.LCE
Retrocopy EKQIQWSQFKGYFIFKLEKVMDDFRTSAPAPRGPPNPNVEYIPFDETKERILKTVTGFNRIPFTIQ*LCE

Parental  LLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKNNSNSLNRMNGVMFPGNSPSYTERSNINGPGTPRP
          LLTDPRRNYTGTDKFL.GVEKNVMVVSCVYPSSEKNNSNSLNRMNGVMFPGN.PSYTERSNINGPGTPRP
Retrocopy LLTDPRRNYTGTDKFLTGVEKNVMVVSCVYPSSEKNNSNSLNRMNGVMFPGNAPSYTERSNINGPGTPRP

Parental  LNR-PKVSLSAPMTTNGLPESTESKEANLQQNEEKNHSDSSTSESEVSSVSPLKNKHPDEDAVEAEGHEV
          LNR..KVSLSAPMTTNG.PEST.SKEANLQQNEEK.HSDSSTSESEVSSV.PLKNKHPDEDAVEAEGHEV
Retrocopy LNR<TKVSLSAPMTTNGWPESTDSKEANLQQNEEKTHSDSSTSESEVSSVNPLKNKHPDEDAVEAEGHEV

Parental  KRLRFDKEGEVRETASQTTSSEISSVMVGETEASSSSQDKDKDSHCTRQ
          KRLRFDK.G.V.ETASQ.T.SEISSVMV.ETEAS.SS.DK.K.S..TRQ
Retrocopy KRLRFDKKGKVGETASQATCSEISSVMVEETEASPSSHDKEKESRGTRQ

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	0.21 RPM	19.16 RPM
SRP007412_cerebellum	0.39 RPM	19.97 RPM
SRP007412_heart	0.03 RPM	29.79 RPM
SRP007412_kidney	0.05 RPM	24.50 RPM
SRP007412_liver	0.03 RPM	21.54 RPM
SRP007412_testis	0.00 RPM	59.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2974 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2974 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2974 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007954	3 retrocopies	retro_chof_1347, retro_chof_1914, retro_chof_2285,
Echinops telfairi	ENSETEG00000019946	2 retrocopies	retro_etel_1238, retro_etel_148,
Homo sapiens	ENSG00000163605	6 retrocopies	retro_hsap_2744, retro_hsap_2745, retro_hsap_2746, retro_hsap_2904, retro_hsap_3138, retro_hsap_3283,
Loxodonta africana	ENSLAFG00000000513	1 retrocopy	retro_lafr_603,
Macaca mulatta	ENSMMUG00000016959	1 retrocopy	retro_mmul_1224,
Mus musculus	ENSMUSG00000052144	3 retrocopies	retro_mmus_1068, retro_mmus_1157, retro_mmus_3474,
Oryctolagus cuniculus	ENSOCUG00000006235	1 retrocopy	retro_ocun_292,
Pan troglodytes	ENSPTRG00000015108	5 retrocopies	retro_ptro_1855, retro_ptro_1856, retro_ptro_2121, retro_ptro_2220, retro_ptro_2974 ,