RetrogeneDB ID: retro_ptro_29

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:133585835..133586606(+)
• Located in intron of: ENSPTRG00000022281

Retrocopy information

• Ensembl ID: ENSPTRG00000039108
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PRDX3
• Ensembl ID: ENSPTRG00000002992
• Aliases: None
• Description: None

Sequence

>retro_ptro_29
ATGGCGGCTGCTGTAGGACGGTTGCTCCGAGCGTCGGTTGCCCGACATGCGAGTGCCATTCCTTGGGGCATTTCTGCCAC
TGCAGCCCTCAGGCCTGCTGCATGTGGAAGAACGAGCTTGACAAATTTATTGTGTTCTGGTTCCAGTCAAGCAAAATTAT
TCAGCACCAGTTCCTCATGCCATGCACCTGCTGTCACCCAGCATGCACCCTATTTTAAGGGTACAGCCATTGTCAATGGA
GAGTTCAAAGACCTAAGCCTTGATGACTTTAAGGGGAAATATTTGGTGCTTTTCTTCTATCCTTTGGATTTCACCTTTGT
GTGTCCTACAGAAATTGTTGCTTTTAGTGACAAAGCTAACGAATTTCACGACGTGAACTGTGAAGTTGTCGCAGTCTCAG
TGGATTCCCACTTTAGCCATCTTGCCTGGATAAATACACCAAGAAAGAATGGTGGTTTGGGCCACATGAACATCGCACTC
TTGTCAGACTTAACTAAGCAGATTTCCCGAGACTACAGTGTGCTGTTAGAAGGTTCTGGTCTTGCACTAAGAGGTCTCTT
CATAATTGACCCCAATGGAGTCATCAAGCACTTAAGCGTCAACGATCTCCCAGTGGGCCGAAGCGTGGAAGAAACCCTCC
GCTTGGTGAAGGCGTTCCAGTATGTAGAAACACATGGAGAAGTCTGCCCAGCGAACTGGACACCGGATTCTCCTACGATC
AAGCCAAGTCCAGCTGCTTCCAAAGAGTACTTTCAGAAGGTAAATCAGTAG

Alignment

ORF - retro_ptro_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVGRLLRASVARHVSAIPWGISATAALRPAACGRTSLTNLLCSGSSQAKLFSTSSSCHAPAVTQHAP
          MAAAVGRLLRASVARH.SAIPWGISATAALRPAACGRTSLTNLLCSGSSQAKLFSTSSSCHAPAVTQHAP
Retrocopy MAAAVGRLLRASVARHASAIPWGISATAALRPAACGRTSLTNLLCSGSSQAKLFSTSSSCHAPAVTQHAP

Parental  YFKGTAVVNGEFKDLSLDDFKGKYLVLFFYPLDFTFVCPTEIVAFSDKANEFHDVNCEVVAVSVDSHFSH
          YFKGTA.VNGEFKDLSLDDFKGKYLVLFFYPLDFTFVCPTEIVAFSDKANEFHDVNCEVVAVSVDSHFSH
Retrocopy YFKGTAIVNGEFKDLSLDDFKGKYLVLFFYPLDFTFVCPTEIVAFSDKANEFHDVNCEVVAVSVDSHFSH

Parental  LAWINTPRKNGGLGHMNIALLSDLTKQISRDYGVLLEGSGLALRGLFIIDPNGVIKHLSVNDLPVGRSVE
          LAWINTPRKNGGLGHMNIALLSDLTKQISRDY.VLLEGSGLALRGLFIIDPNGVIKHLSVNDLPVGRSVE
Retrocopy LAWINTPRKNGGLGHMNIALLSDLTKQISRDYSVLLEGSGLALRGLFIIDPNGVIKHLSVNDLPVGRSVE

Parental  ETLRLVKAFQYVETHGEVCPANWTPDSPTIKPSPAASKEYFQKVNQ
          ETLRLVKAFQYVETHGEVCPANWTPDSPTIKPSPAASKEYFQKVNQ
Retrocopy ETLRLVKAFQYVETHGEVCPANWTPDSPTIKPSPAASKEYFQKVNQ

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	1.27 RPM	31.85 RPM
SRP007412_cerebellum	0.04 RPM	7.03 RPM
SRP007412_heart	0.20 RPM	37.13 RPM
SRP007412_kidney	0.34 RPM	65.35 RPM
SRP007412_liver	0.23 RPM	25.60 RPM
SRP007412_testis	0.00 RPM	3.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_29 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_29 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus	ENSCJAG00000019636	3 retrocopies	retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi	ENSCSAVG00000001209	1 retrocopy	retro_csav_6,
Dasypus novemcinctus	ENSDNOG00000001359	3 retrocopies	retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus	ENSECAG00000017026	1 retrocopy	retro_ecab_408,
Erinaceus europaeus	ENSEEUG00000009299	1 retrocopy	retro_eeur_238,
Homo sapiens	ENSG00000165672	3 retrocopies	retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Macropus eugenii	ENSMEUG00000007732	3 retrocopies	retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus	ENSMICG00000007627	1 retrocopy	retro_mmur_475,
Myotis lucifugus	ENSMLUG00000012871	3 retrocopies	retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica	ENSMODG00000009286	1 retrocopy	retro_mdom_1062,
Mustela putorius furo	ENSMPUG00000003074	1 retrocopy	retro_mputfur_1032,
Mus musculus	ENSMUSG00000024997	1 retrocopy	retro_mmus_2443,
Nomascus leucogenys	ENSNLEG00000016698	3 retrocopies	retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus	ENSOCUG00000017334	2 retrocopies	retro_ocun_135, retro_ocun_1434,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pan troglodytes	ENSPTRG00000000675	1 retrocopy	retro_ptro_2874,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29 ,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Ictidomys tridecemlineatus	ENSSTOG00000002537	2 retrocopies	retro_itri_1098, retro_itri_1753,
Tupaia belangeri	ENSTBEG00000011064	5 retrocopies	retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus	ENSTTRG00000010878	2 retrocopies	retro_ttru_1703, retro_ttru_881,