RetrogeneDB ID: retro_ptro_659

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:7052219..7052672(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSTN
• Ensembl ID: ENSPTRG00000013275
• Aliases: None
• Description: None

Sequence

>retro_ptro_659
GCCTCAGGAGTGCAAGTTGCTGATGAAGTATGTCGCATTTTTTATGACATGAGAGTTCGTAAATGCTCCACACCAGAAGA
AATCAAGAAAAGAACAAAGGCTGTCATTTTTTTGTCTCAGTGCAGACAAAAAGTGCATCATGTAGAAGGCAAAGAGGTCT
TGGTTGGAGATGTTGGTGTAACTATAAGTGAGCCTTTCAAGCATTTTGTGGGAATGCTTCCTGAAAAAGATTGTTGCTAT
GTTTTGTATGATGCAAGCTTTGAAACAAAAGAATCCAGAAGAATTGATGTTTTCTTGTGGGCATCAGAACTAGCACCTTT
GAAAAGTAAAATGATCTATACAAGCTCCAAGGATGCAATCAAAAAGAAATTTCAAGGCATAAAACATGAATGGCAAACAA
ACGGACCAGAAGATCTCAATCGGGCTTGTACTGCTGAAAAGTTAGGTGGATCC

Alignment

ORF - retro_ptro_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.9 %
• Parental protein coverage: 93.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASGVQVADEVCRIFYDMKVRKCSTPEEIKKRKKAVI-FCLSADKKCII-VEEGKEILVGDVGVTITDPFK
          ASGVQVADEVCRIFYDM.VRKCSTPEEIKKR.KAVI.FCLSADKKCI..VE.GKE.LVGDVGVTI..PFK
Retrocopy ASGVQVADEVCRIFYDMRVRKCSTPEEIKKRTKAVI>FCLSADKKCIM<VE-GKEVLVGDVGVTISEPFK

Parental  HFVGMLPEKDCRYALYDASFETKESRKEELMFFLWAPELAPLKSKMIYASSKDAIKKKFQGIKHECQANG
          HFVGMLPEKDC.Y.LYDASFETKESR......FLWA.ELAPLKSKMIY.SSKDAIKKKFQGIKHE.Q.NG
Retrocopy HFVGMLPEKDCCYVLYDASFETKESRRIDV--FLWASELAPLKSKMIYTSSKDAIKKKFQGIKHEWQTNG

Parental  PEDLNRACIAEKLGGS
          PEDLNRAC.AEKLGGS
Retrocopy PEDLNRACTAEKLGGS

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	0.00 RPM	128.80 RPM
SRP007412_cerebellum	0.04 RPM	71.95 RPM
SRP007412_heart	0.00 RPM	173.59 RPM
SRP007412_kidney	0.00 RPM	158.32 RPM
SRP007412_liver	0.00 RPM	32.70 RPM
SRP007412_testis	0.00 RPM	44.58 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_659 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_659 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_952
Pongo abelii	retro_pabe_812
Macaca mulatta	retro_mmul_782

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880,
Choloepus hoffmanni	ENSCHOG00000003110	5 retrocopies	retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72,
Cavia porcellus	ENSCPOG00000005573	2 retrocopies	retro_cpor_700, retro_cpor_812,
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Erinaceus europaeus	ENSEEUG00000011893	1 retrocopy	retro_eeur_529,
Homo sapiens	ENSG00000125868	1 retrocopy	retro_hsap_952,
Gorilla gorilla	ENSGGOG00000009007	1 retrocopy	retro_ggor_768,
Microcebus murinus	ENSMICG00000013687	1 retrocopy	retro_mmur_765,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Nomascus leucogenys	ENSNLEG00000009679	1 retrocopy	retro_nleu_2458,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891,
Ochotona princeps	ENSOPRG00000000976	2 retrocopies	retro_opri_1078, retro_opri_696,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000003895	5 retrocopies	retro_ptro_1764, retro_ptro_2146, retro_ptro_236, retro_ptro_298, retro_ptro_306,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659 ,
Pteropus vampyrus	ENSPVAG00000000420	1 retrocopy	retro_pvam_1275,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Sus scrofa	ENSSSCG00000007085	1 retrocopy	retro_sscr_954,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus	ENSTTRG00000007291	1 retrocopy	retro_ttru_1503,