RetrogeneDB ID: retro_ptro_979

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:67577143..67577630(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIF
• Ensembl ID: ENSPTRG00000002669
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:H2Q253]

Sequence

>retro_ptro_979
AACCCCACCATGTTCTTTGAATTTGCCGTCGACAGCAAGCCCTTGGGCCATGTCTCCTTCGAGCTGTTTGCAGACAAGAT
CCCAAAGACAGCAGAAAATTTTCGTGCTCCAAGCACTGGAGAGAAAGGATTTGGTTATAAGGGTTCCTGCTTTCACAGAA
TTATTCCAGGGTTTATGTGTCAGGGTGGTGACTGTGAAGTCATCATAATGGCACTGGTGGCAAGTCCATCTACACGGAGA
AATTTGAAGATGAGAACTTCATCCTAAAGCATACAGGTCCTGGCATCTTGTCCATGGCAAATGCTGGACCCAACACAAAT
GGTTCCCAGTTTTTCATCTGCACTGCCAAGACTGAGTGGTTGGATGGCAAGCATGTGCTCTTTGGCAAAGTGAAAGAAGG
CATGAATATTGTGGAGGCATGGAGCGCTTTGGGTCCAGGAATGGCAAGACCAGCAAGAAGATCACCATTGCTGACTGTGG
ACAACTC

Alignment

ORF - retro_ptro_979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.27 %
• Parental protein coverage: 78.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFT-NHN
          NP..........KPLG.V..EL.AD..PKTAENFRA..TGEKGFGYKGS.FHR.IP.FMCQ.GD....H.
Retrocopy NPTMFFEFAVDSKPLGHVSFELFADKIPKTAENFRAPSTGEKGFGYKGSCFHRIIPGFMCQGGDCE<SHH

Parental  GTGG-KSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVKEGMDVVK
          ...G.KSIY...F.DENF.LKH.GPG.LSMANAGPNTNGSQFFICT.KT.WLDGKHV.FG.VKEGM..V.
Retrocopy NGTGGKSIYTEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVLFGKVKEGMNIVE

Parental  K-IESFGSKSGRTSKKIVITDCGQL
          ...E.FGS..G.TSKKI.I.DCGQL
Retrocopy A<MERFGSRNGKTSKKITIADCGQL

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	0.43 RPM	59.99 RPM
SRP007412_cerebellum	0.04 RPM	33.45 RPM
SRP007412_heart	0.00 RPM	73.27 RPM
SRP007412_kidney	0.03 RPM	82.20 RPM
SRP007412_liver	0.23 RPM	125.67 RPM
SRP007412_testis	0.00 RPM	21.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_979 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_979 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1436
Pongo abelii	retro_pabe_186

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008796	3 retrocopies	retro_ecab_507, retro_ecab_649, retro_ecab_732,
Homo sapiens	ENSG00000108179	1 retrocopy	retro_hsap_1436,
Microcebus murinus	ENSMICG00000007086	8 retrocopies	retro_mmur_1266, retro_mmur_218, retro_mmur_515, retro_mmur_568, retro_mmur_605, retro_mmur_694, retro_mmur_769, retro_mmur_87,
Nomascus leucogenys	ENSNLEG00000010567	1 retrocopy	retro_nleu_70,
Procavia capensis	ENSPCAG00000009406	1 retrocopy	retro_pcap_275,
Pan troglodytes	ENSPTRG00000002669	1 retrocopy	retro_ptro_979 ,
Pan troglodytes	ENSPTRG00000023064	77 retrocopies	retro_ptro_1116, retro_ptro_1122, retro_ptro_1124, retro_ptro_1213, retro_ptro_1277, retro_ptro_1328, retro_ptro_1377, retro_ptro_1399, retro_ptro_1401, retro_ptro_1423, retro_ptro_1449, retro_ptro_1463, retro_ptro_1529, retro_ptro_1531, retro_ptro_1544, retro_ptro_1596, retro_ptro_1626, retro_ptro_1639, retro_ptro_1672, retro_ptro_1717, retro_ptro_1779, retro_ptro_1787, retro_ptro_1835, retro_ptro_1843, retro_ptro_1889, retro_ptro_1890, retro_ptro_1891, retro_ptro_1916, retro_ptro_1925, retro_ptro_195, retro_ptro_1952, retro_ptro_2012, retro_ptro_2014, retro_ptro_210, retro_ptro_2136, retro_ptro_2138, retro_ptro_2161, retro_ptro_2260, retro_ptro_2272, retro_ptro_2425, retro_ptro_2546, retro_ptro_2562, retro_ptro_2611, retro_ptro_2642, retro_ptro_2663, retro_ptro_2689, retro_ptro_2692, retro_ptro_278, retro_ptro_2806, retro_ptro_2899, retro_ptro_2904, retro_ptro_2914, retro_ptro_293, retro_ptro_2945, retro_ptro_2967, retro_ptro_3010, retro_ptro_3033, retro_ptro_3049, retro_ptro_326, retro_ptro_394, retro_ptro_458, retro_ptro_472, retro_ptro_477, retro_ptro_498, retro_ptro_518, retro_ptro_521, retro_ptro_527, retro_ptro_541, retro_ptro_567, retro_ptro_585, retro_ptro_783, retro_ptro_825, retro_ptro_853, retro_ptro_879, retro_ptro_889, retro_ptro_905, retro_ptro_921,
Pteropus vampyrus	ENSPVAG00000001713	2 retrocopies	retro_pvam_380, retro_pvam_623,
Tupaia belangeri	ENSTBEG00000015457	1 retrocopy	retro_tbel_1906,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20,