RetrogeneDB ID: retro_ptro_3227

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:64952140..64952784(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AAED1
• Ensembl ID: ENSPTRG00000021156
• Aliases: None
• Description: AhpC/TSA antioxidant enzyme domain containing 1 [Source:HGNC Symbol;Acc:16881]

Sequence

>retro_ptro_3227
AGTGGTGGTGTTGCCTGTGTCCAGGCCCTGAGTGGCCCTGAACATGGGCAGCCCCTGGTAGCTGCCATAGCCGAGCTGCC
AGTGCTGGACTCTCATGCGCAGTGGGTGCCATTTGGAGCTCTCCTCTGGGAGCGCCACACTATGGTAGTGTTTGTGCAAC
ATTTCCTGTTTTACATTTGCAAGGAATATGTAGAGGATCTGCCCAAAATCCCAAAGAGTTTCCTACAAGAAGCAAATGTC
ACTCTTATAGTGATTGAACAGTCATCCTACCATCCTATTGAGTCTTTCTGCAAACTGCCTGGATATTCTCATGAAATCTA
TTTCACCCTGAGAGGGAAATTTATAACAGATTGGGAATGAAAAGAGGTGAAGAAATGGCCTCCTCAGGACAGAGCCCCCA
TGTGAAGTCAAATATACTCTCAGGAAGCCTTTGGAGCTTGTGGTGGGCAGTGACTGGCCCTCTCTTTGATTTTCAAGGAG
ACCCAGCTCAGCAAGGTGGAACTTTCATTTTAGGTCCAGGTAACAACATCCATTTTATACACCATGAGAGGAATATGTTG
GATCACAAACCTATCAACTCTGTTTTACAGCCTGTGGGAGTTTAGCATGTGAACTTTACAAACAGATCTTCAATTATCCA
TGTG

Alignment

ORF - retro_ptro_3227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.02 %
• Parental protein coverage: 95.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGAAALVPAPSGPDSGQPLAAAVAELPVLDARGQRVPFGALFRERRAVVVFVRHFLCYICKEYVEDLAKI
          SG..A.V.A.SGP..GQPL.AA.AELPVLD...Q.VPFGAL..ER...VVFV.HFL.YICKEYVEDL.KI
Retrocopy SGGVACVQALSGPEHGQPLVAAIAELPVLDSHAQWVPFGALLWERHTMVVFVQHFLFYICKEYVEDLPKI

Parental  PKSFLQEANVTLIVIGQSSYHHIEPFCKLTGYSHEIYVD-PEREIYKRLGMKRGEEIASSGQSPHVKSNL
          PKSFLQEANVTLIVI.QSSYH.IE.FCKL.GYSHEIY...PEREIY.RLGMKRGEE.ASSGQSPHVKSN.
Retrocopy PKSFLQEANVTLIVIEQSSYHPIESFCKLPGYSHEIYFT<PEREIYNRLGMKRGEEMASSGQSPHVKSNI

Parental  LSGSLQSLWRAVTGPLFDFQGDPAQQGGTLILGPGNNIHFIHRDRNRLDHKPINSVLQLVGVQHVNFTNR
          LSGSL.SLW.AVTGPLFDFQGDPAQQGGT.ILGPGNNIHFIH..RN.LDHKPINSVLQ.VGV.HVNFTNR
Retrocopy LSGSLWSLWWAVTGPLFDFQGDPAQQGGTFILGPGNNIHFIHHERNMLDHKPINSVLQPVGV*HVNFTNR

Parental  PSVIHV
          .S.IHV
Retrocopy SSIIHV

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	0.00 RPM	2.18 RPM
SRP007412_cerebellum	0.00 RPM	1.65 RPM
SRP007412_heart	0.00 RPM	10.75 RPM
SRP007412_kidney	0.00 RPM	7.69 RPM
SRP007412_liver	0.00 RPM	7.40 RPM
SRP007412_testis	0.00 RPM	6.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3227 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3227 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4843
Pongo abelii	retro_pabe_3765

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006422	1 retrocopy	retro_chof_1792,
Choloepus hoffmanni	ENSCHOG00000007723	7 retrocopies	retro_chof_1026, retro_chof_1037, retro_chof_1808, retro_chof_2079, retro_chof_2149, retro_chof_2642, retro_chof_811,
Callithrix jacchus	ENSCJAG00000005509	1 retrocopy	retro_cjac_4168,
Dasypus novemcinctus	ENSDNOG00000024562	4 retrocopies	retro_dnov_1226, retro_dnov_1419, retro_dnov_1519, retro_dnov_1871,
Homo sapiens	ENSG00000158122	1 retrocopy	retro_hsap_4843,
Macaca mulatta	ENSMMUG00000008295	1 retrocopy	retro_mmul_2586,
Otolemur garnettii	ENSOGAG00000017058	1 retrocopy	retro_ogar_1866,
Procavia capensis	ENSPCAG00000003177	1 retrocopy	retro_pcap_269,
Pongo abelii	ENSPPYG00000019418	1 retrocopy	retro_pabe_3765,
Pan troglodytes	ENSPTRG00000021156	1 retrocopy	retro_ptro_3227 ,