RetrogeneDB ID: retro_ptro_2217

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:180709842..180710379(+)
• Located in intron of: ENSPTRG00000017616

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX2
• Ensembl ID: ENSPTRG00000010541
• Aliases: None
• Description: None

Sequence

>retro_ptro_2217
ATGGCTTCCAGTCAGTCGCAGCTCGGAAAGCCAGCCCCTGACTTCAAGGCCATCGCCCTGGTGGATGGCGCCTTCCAGGA
GGTGAAGCTGTGGGCTACAAAGGGAAGTACGTCATCCTCTTTTTCTACCCTCTGGACTTCACTTTTCTGTGGCCCATGGA
GAACGTCGCATTCAGCGACCATGCCGAGGATTTCCGCAAGCTGGGCTGCGAAGTGCTGGGTGTCTGGGTGGACTTAGTTC
ACCCACCTGGCTTGGATCAACAACCCCCAGAAGTAGGGAGGCTTAGGCTCCCGAGCATCCCCCACCCGTTGATGTGACGG
GAAGCTTGTCTGAGGATTACCGTGTGCTGAAAACCAATGAGGGCATTGCCTACCCTGCCTCTTTATCATCGATGGCAAGG
GAGACTTTTGCCAGATCACTGTTAATGATTTGCCTCTGGGGTGCTCCATGGATGAGGCTCTGCAGCTGGTCCAGGCATTC
CAGTACGCAGATGAGCACGGGGAAGTTTGTCCCACTGGCTGGAAGCCTGGTAGCGAC

Alignment

ORF - retro_ptro_2217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.2 %
• Parental protein coverage: 91.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MASGNARIGKPAPDFKATAVVDGAFKEVKL-SDYKGKYVVLFFYPLDFTFVCPTEIIAFSNRAED-FRKL
          MAS.....GKPAPDFKA.A.VDGAF.EVKL...YKGKYV.LFFYPLDFTF..P.E..AFS..AED.F...
Retrocopy MASSQSQLGKPAPDFKAIALVDGAFQEVKL<VGYKGKYVILFFYPLDFTFLWPMENVAFSDHAED<FPQA

Parental  GCEVLG-VSVDSQFTHLAWIN-TPRKEGGLGPLNIPLLADVTRRLSEDYGVLKTDEGIAYRG-LFIIDGK
          G....G.VS....FTHLAWIN.TPR......P...P...DVT..LSEDY.VLKT.EGIAY...LFIIDGK
Retrocopy GLRSAG<VSGWT*FTHLAWIN>TPRSREA*APEHPPPV-DVTGSLSEDYRVLKTNEGIAYPA<LFIIDGK

Parental  GVLRQITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSD
          G...QITVNDLP.G.S.DEAL.LVQAFQY.DEHGEVCP.GWKPGSD
Retrocopy GDFCQITVNDLPLGCSMDEALQLVQAFQYADEHGEVCPTGWKPGSD

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	0.29 RPM	248.54 RPM
SRP007412_cerebellum	0.29 RPM	154.61 RPM
SRP007412_heart	0.00 RPM	162.69 RPM
SRP007412_kidney	0.03 RPM	171.84 RPM
SRP007412_liver	0.03 RPM	66.52 RPM
SRP007412_testis	0.00 RPM	6.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2217 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2217 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3278
Pongo abelii	retro_pabe_2711
Callithrix jacchus	retro_cjac_1795

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184, retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
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,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,