RetrogeneDB ID: retro_ptro_2063

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:83628171..83628331(-)
• Located in intron of: ENSPTRG00000016042

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM2
• Ensembl ID: ENSPTRG00000017986
• Aliases: None
• Description: None

Sequence

>retro_ptro_2063
ATGCTCTTCTATTCCTTTTTCAATCCCTATGGGCAAGGATGTAAACCTGGAACTCAAGAATGACCTGCTTATCTGTGGAC
CCCTGCATTCTGTGGATCAGTATCTCAACATCAGATTAACTAACATCAGCGTTACAGACCCTGAGAAATACCCTCACATC

Alignment

ORF - retro_ptro_2063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.36 %
• Parental protein coverage: 56.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLFYSF-FKSL-VGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHM
          MLFYSF.F.SL..GKDV..ELKNDL.ICG.LHSVDQYLNI.LT.ISVTDPEKYPH.
Retrocopy MLFYSF<FQSL<MGKDVNLELKNDLLICGPLHSVDQYLNIRLTNISVTDPEKYPHI

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	0.09 RPM	11.44 RPM
SRP007412_cerebellum	0.00 RPM	13.41 RPM
SRP007412_heart	0.00 RPM	7.72 RPM
SRP007412_kidney	0.05 RPM	15.53 RPM
SRP007412_liver	0.03 RPM	8.74 RPM
SRP007412_testis	0.11 RPM	9.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2063 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2063 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2063 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2928
Macaca mulatta	retro_mmul_1875

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002601	2 retrocopies	retro_cjac_1828, retro_cjac_2088,
Felis catus	ENSFCAG00000004511	1 retrocopy	retro_fcat_309,
Macaca mulatta	ENSMMUG00000006832	3 retrocopies	retro_mmul_1389, retro_mmul_1875, retro_mmul_2099,
Mus musculus	ENSMUSG00000007050	1 retrocopy	retro_mmus_931,
Nomascus leucogenys	ENSNLEG00000006371	1 retrocopy	retro_nleu_960,
Ochotona princeps	ENSOPRG00000003668	2 retrocopies	retro_opri_250, retro_opri_917,
Pongo abelii	ENSPPYG00000016461	1 retrocopy	retro_pabe_2765,
Pan troglodytes	ENSPTRG00000017986	3 retrocopies	retro_ptro_1349, retro_ptro_2063 , retro_ptro_2284,
Rattus norvegicus	ENSRNOG00000048725	1 retrocopy	retro_rnor_1463,
Ictidomys tridecemlineatus	ENSSTOG00000013144	1 retrocopy	retro_itri_189,