RetrogeneDB ID: retro_ptro_644

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:109936427..109936957(-)
• Located in intron of: ENSPTRG00000004279

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIH
• Ensembl ID: ENSPTRG00000000614
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:H2PYT6]

Sequence

>retro_ptro_644
ATGGTGGTGGCAACTTCAAGCCCTGCTAACCCCATGGTGTTCTTTGATGTCAGCAATGGCAGTCAGGAAGTTGGCCGCAC
AAAGATCGAGCTCTCTGCAGACGCTGTGCCTAAGACGACCGAGAACTTTGGGTAGTTCTGCACTAGAGAATTCAGAAAAG
ATGGGGTTCCAATAGGATACAAAGGAAGCACTTTCCACAGGGTTATAAAGGATTTCATGATTTAGGGTGGAGATTTTGTT
AATGGAGATGGTACTGGAGTCGCCAGTATTTACCAGGAGACATTCGCAGATGAAAATTTTAAACTTAGACACTCAGCTCC
AGGCCTGCTTTCCACGGCAAACAGCGGTCCCAGTACAAATGGCTGTCAGTTCTTTATCACCTGCTCTAAGTGTGATTGGC
TGGATGGGAAGCATGTAATGTTTGGAAAAATCACTGATGGACTTCTAGTGATGAAAAAGATTCAGAATGTTCCCACAGGC
CCCAACAATAAGCCCAAACTACTGTAGTGATCTCAAAGTGCGGGGAGATG

Alignment

ORF - retro_ptro_644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIK
          M.VA.SSP.NP.VFFDVS.G.QEVGR.KIEL.AD.VPKT.ENF..FCT.EFRKDGVPIGYKGSTFHRVIK
Retrocopy MVVATSSPANPMVFFDVSNGSQEVGRTKIELSADAVPKTTENFG*FCTREFRKDGVPIGYKGSTFHRVIK

Parental  DFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVV
          DFMI.GGDFVNGDGTGVASIY...FADENFKLRHSAPGLLS.ANSGPSTNGCQFFITCSKCDWLDGKHV.
Retrocopy DFMI*GGDFVNGDGTGVASIYQETFADENFKLRHSAPGLLSTANSGPSTNGCQFFITCSKCDWLDGKHVM

Parental  FGKIIDGLLVMRKIENVPTGPNNKPKL-PVVISQCGEM
          FGKI.DGLLVM.KI.NVPTGPNNKPKL..VVIS.CGEM
Retrocopy FGKITDGLLVMKKIQNVPTGPNNKPKL<TVVISKCGEM

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	0.11 RPM	9.40 RPM
SRP007412_cerebellum	0.04 RPM	14.59 RPM
SRP007412_heart	0.09 RPM	10.35 RPM
SRP007412_kidney	0.05 RPM	12.74 RPM
SRP007412_liver	0.03 RPM	10.25 RPM
SRP007412_testis	0.00 RPM	11.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_644 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_644 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_644 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_928
Gorilla gorilla	retro_ggor_748
Pongo abelii	retro_pabe_797
Macaca mulatta	retro_mmul_1124

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000526	1 retrocopy	retro_amel_1481,
Bos taurus	ENSBTAG00000004590	1 retrocopy	retro_btau_1530,
Callithrix jacchus	ENSCJAG00000003145	5 retrocopies	retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Cavia porcellus	ENSCPOG00000008214	8 retrocopies	retro_cpor_1511, retro_cpor_785, retro_cpor_786, retro_cpor_794, retro_cpor_795, retro_cpor_796, retro_cpor_797, retro_cpor_798,
Dipodomys ordii	ENSDORG00000016152	3 retrocopies	retro_dord_151, retro_dord_173, retro_dord_447,
Homo sapiens	ENSG00000171960	2 retrocopies	retro_hsap_4740, retro_hsap_928,
Gorilla gorilla	ENSGGOG00000022507	2 retrocopies	retro_ggor_2945, retro_ggor_748,
Macropus eugenii	ENSMEUG00000001691	1 retrocopy	retro_meug_1699,
Myotis lucifugus	ENSMLUG00000025400	2 retrocopies	retro_mluc_1922, retro_mluc_2243,
Macaca mulatta	ENSMMUG00000013129	1 retrocopy	retro_mmul_1124,
Mustela putorius furo	ENSMPUG00000013966	2 retrocopies	retro_mputfur_285, retro_mputfur_542,
Nomascus leucogenys	ENSNLEG00000012313	2 retrocopies	retro_nleu_1242, retro_nleu_289,
Oryctolagus cuniculus	ENSOCUG00000011453	1 retrocopy	retro_ocun_1195,
Procavia capensis	ENSPCAG00000011139	1 retrocopy	retro_pcap_81,
Pongo abelii	ENSPPYG00000001467	2 retrocopies	retro_pabe_3686, retro_pabe_797,
Pan troglodytes	ENSPTRG00000000614	2 retrocopies	retro_ptro_3155, retro_ptro_644 ,
Pan troglodytes	ENSPTRG00000018111	1 retrocopy	retro_ptro_1535,
Pteropus vampyrus	ENSPVAG00000005500	1 retrocopy	retro_pvam_107,
Ictidomys tridecemlineatus	ENSSTOG00000000115	2 retrocopies	retro_itri_1248, retro_itri_412,
Tarsius syrichta	ENSTSYG00000003182	2 retrocopies	retro_tsyr_224, retro_tsyr_647,