RetrogeneDB ID: retro_pabe_1906

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:33914308..33914806(-)
• Located in intron of: ENSPPYG00000011827

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX3
• Ensembl ID: ENSPPYG00000002700
• Aliases: None
• Description: Thioredoxin-dependent peroxide reductase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5REY3]

Sequence

>retro_pabe_1906
ATGGTAGCTGCTGTGGGAAGGCTGCTCTGAGCATCGGTTGCCCGACATGTGAGTGCCATTCCTTGGGGCATTTCTGCCAC
TGCAGCCCTCAAGCTTGCTGCTTCTGGAAGAACGGGCTTGACAAACATATTATGGTCTAGTTCCGGTCAAGCAAAATTCT
TTAGCACCAGCTCCTCATACCATGCACCTGCTGTCGCCCAGCATGCACCCTATTTTAAGGGTACAGCCATTGTCAATGGA
GAGTTCAAAGACCTAAGCCTTGATGACTTCAAGGGGAAATAATTTGGTGCTTTTCTTCTATCCTTTGGATTTCACCTTTG
TGGTCCTACAGAAACTGTTGCTTTTAGTGACAAAGCTAAGGAATTTCATGATGTGAACTGTGAAGTTGTTGTGGTCTCAG
TGAATTCCCACTTTAGTCATCTTGCCTGGATAAATACACCAAGAAATAATGGTGGTTTGGACCACATGAACATCCCACTC
TTGTCAGATTTGAGCAAA

Alignment

ORF - retro_pabe_1906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.52 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAVGRLLRASVARGVSAIPWGISATAALRPAACGRTSLTNLLCSGSSQAKLFSTSSSYHAPAVTQHAP
          M.AAVGRLL.ASVAR.VSAIPWGISATAAL..AA.GRT.LTN.L.S.S.QAK.FSTSSSYHAPAV.QHAP
Retrocopy MVAAVGRLL*ASVARHVSAIPWGISATAALKLAASGRTGLTNILWSSSGQAKFFSTSSSYHAPAVAQHAP

Parental  YFKGTAVVNGEFKDLSLDDFKGK-YLVLFFYPLDFTFVC-PTEIVAFSDKANEFHDVNCEVVAVSVDSHF
          YFKGTA.VNGEFKDLSLDDFKGK..LVLFFYPLDFTFV..PTE.VAFSDKA.EFHDVNCEVV.VSV.SHF
Retrocopy YFKGTAIVNGEFKDLSLDDFKGK>NLVLFFYPLDFTFVV<PTETVAFSDKAKEFHDVNCEVVVVSVNSHF

Parental  SHLAWINTPRKNGGLGHMNIALLSDLTK
          SHLAWINTPR.NGGL.HMNI.LLSDL.K
Retrocopy SHLAWINTPRNNGGLDHMNIPLLSDLSK

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	0.33 RPM	43.79 RPM
SRP007412_cerebellum	0.61 RPM	57.40 RPM
SRP007412_heart	0.30 RPM	79.35 RPM
SRP007412_kidney	0.53 RPM	74.68 RPM
SRP007412_liver	0.70 RPM	75.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1906 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1906 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 48 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,
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	ENSPPYG00000001411	1 retrocopy	retro_pabe_3409,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906 ,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29,
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,