RetrogeneDB ID: retro_ptro_1622

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:91449684..91450271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SETD8
• Ensembl ID: ENSPTRG00000005598
• Aliases: None
• Description: None

Sequence

>retro_ptro_1622
GCTGCAGGCAGGAAGATGTCCAAGCCCCGAACGCTGGAGGCGGCGGCGGCGGCGGCATCGACGGCCCCGGGCCTGGAGAT
GGTGGAGCGGAGGGGCCCGGGGAGGCCCCGCACCGATGGGGAGAACGTATTTACCGGGCAGTCAAAGATCTATTCCTACA
TGAGCCCGAACAAATGCTCTGAATGCGTTTCCCCCTTCAGGAAGAGAACTCAGTTACACATCACGAAGTCAAATGCCAGG
GGAAACCATTAGCCGGAATCTACAGGAAACGAGAAGAGAAAAGAAATACTGGGAACGCAGTACGGAGCGCCATGAAGTCC
AAGGAACAGAAGATCAAAGACGCCAGGAGAGGTCCCCTGGTACCTTTTCCAAACCAAAAATCTGAAGCAGCAGAACCTCC
AAAAACTCCACCCTCATCTTGTGATTCCACCAATGCAGCCATCGCCAAGCAAGCCCTGAAAAAGCCCATCAAGGGCAAAC
AGGCCCCCCGAAAAAAAGCTCAAGGAAAAACGCAACAGAATCACAAACTTACGGATTTCTACCCTGTCCGAAGGAGATCC
AGGAAGAGGAAAGCCGAGCTGCAGTCT

Alignment

ORF - retro_ptro_1622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 56.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARGRKMSKPRAVEAAAAAAAVAATAPGPEMVERRGPGRPRTDGENVFTGQSKIYSYMSPNKCSG-MRFPL
          A.GRKMSKPR..EAAAAA...A.TAPG.EMVERRGPGRPRTDGENVFTGQSKIYSYMSPNKCS..MRFPL
Retrocopy AAGRKMSKPRTLEAAAAA---ASTAPGLEMVERRGPGRPRTDGENVFTGQSKIYSYMSPNKCSE<MRFPL

Parental  QEENSVTHHEVKCQGKPLAGIYRKREEKRNAGNAVRSAMKSEEQKIKDARRGPLVPFPNQKSEAAEPPKT
          QEENSVTHHEVKCQGKPLAGIYRKREEKRN.GNAVRSAMKS.EQKIKDARRGPLVPFPNQKSEAAEPPKT
Retrocopy QEENSVTHHEVKCQGKPLAGIYRKREEKRNTGNAVRSAMKSKEQKIKDARRGPLVPFPNQKSEAAEPPKT

Parental  PPSSCDSTNAAIAKQALKKPIKGKQAPRKKAQGKTQQNRKLTDFYPVRRSSRKSKAELQS
          PPSSCDSTNAAIAKQALKKPIKGKQAPRKKAQGKTQQN.KLTDFYPVRR.SRK.KAELQS
Retrocopy PPSSCDSTNAAIAKQALKKPIKGKQAPRKKAQGKTQQNHKLTDFYPVRRRSRKRKAELQS

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	26.44 RPM
SRP007412_cerebellum	0.82 RPM	19.68 RPM
SRP007412_heart	0.41 RPM	20.31 RPM
SRP007412_kidney	0.31 RPM	20.63 RPM
SRP007412_liver	0.75 RPM	19.90 RPM
SRP007412_testis	0.00 RPM	7.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1622 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1622 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1622 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183955	2 retrocopies	retro_hsap_2294, retro_hsap_4320,
Macaca mulatta	ENSMMUG00000013514	1 retrocopy	retro_mmul_1579,
Mus musculus	ENSMUSG00000049327	2 retrocopies	retro_mmus_1459, retro_mmus_3478,
Otolemur garnettii	ENSOGAG00000031093	1 retrocopy	retro_ogar_1217,
Pongo abelii	ENSPPYG00000005085	2 retrocopies	retro_pabe_1347, retro_pabe_1381,
Pan troglodytes	ENSPTRG00000005598	1 retrocopy	retro_ptro_1622 ,
Rattus norvegicus	ENSRNOG00000001062	4 retrocopies	retro_rnor_1551, retro_rnor_2837, retro_rnor_38, retro_rnor_679,
Sarcophilus harrisii	ENSSHAG00000015376	2 retrocopies	retro_shar_110, retro_shar_115,
Tursiops truncatus	ENSTTRG00000015884	1 retrocopy	retro_ttru_1301,