RetrogeneDB ID: retro_ptro_2047

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:40078785..40079676(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACOT7
• Ensembl ID: ENSPTRG00000000084
• Aliases: None
• Description: None

Sequence

>retro_ptro_2047
CGGATTATGCGGCCAGATGACGCCAATGTGGCCCGCAATGTCTAGGCGGGGACCATCCTGAAGATGATCAAAGAGGCGGG
CGCCATTATCAGCACCCGGCATTGCAACCCGCAGAACGGGGATCGCTGTGTGGCCGCTCTGGCTCGGGTCGAGTGCACCG
ACTTCCTGTGGCCCATGTGCATCGGTGAGGTGGCCCACGTCAGCGCGGAGATCACCTACACCTCCAAGCACTCTGTGGAG
GTGCAGGTCAACATGATGTCCGAAAACATCCTCACAGGTGCCAAAAAGCTGACCAATAAGGCCACCCTCTGGTATGCGCC
CCTGTCGCTGACGAACGTGGACAAGGTCCTCGAAGAGCCTCCTGTTGTGTATTTCCGGCAGGAGCAGGAGGAGGAGGTTC
AGAAGCGGTACAAAACCCAGAAGCTGGAGCGCATGGAGACCAACTGGAGGAACGGGGACATCGTCCAGCCAGTCCTCAAC
CCAGAGCCGAACACTGTCAGCTACAGCCAGTCCAGCTTGATCCACCTGGTGGGGCCTTCAGACTGTACCCTGCACAGCTT
CATGCATGAAGGCTTGACCATGAAGGTCATGGACGAGGTCGCCGGGATCTTGGCTGCACGCCACTGCAAGACCAACCTCA
ACACAGCCTCCATGGAGGCCATTAATTTTGACAACAAGATCAGAAAAGTCTGCATCAAGACCATCTCCGGACGCATGACG
TTCACGAGCAATAAGTCCGTAGAGATCGAGGTCTTGGTGGATGCCGACTGTGTTGTGGACAGCTCTCAGAAGCGCTACCG
GGCCGCCGGTGTCTTCACCTAAGTGTCGCTGAGCCAGGAAGGCAGGTCGCTGCCCATGCCCCAGCTCGTGCCGGAGACCC
AGGACGAGAAG

Alignment

ORF - retro_ptro_2047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.24 %
• Parental protein coverage: 78.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RIMRPDDANVAGNVHGGTILKMIEEAGAIISTRHCNSQNGERCVAALARVERTDFLSPMCIGEVAHVSAE
          RIMRPDDANVA.NV..GTILKMI.EAGAIISTRHCN.QNG.RCVAALARVE.TDFL.PMCIGEVAHVSAE
Retrocopy RIMRPDDANVARNV*AGTILKMIKEAGAIISTRHCNPQNGDRCVAALARVECTDFLWPMCIGEVAHVSAE

Parental  ITYTSKHSVEVQVNVMSENILTGAKKLTNKATLWYVPLSLKNVDKVLEVPPVVYSRQEQEEEGRKRYEAQ
          ITYTSKHSVEVQVN.MSENILTGAKKLTNKATLWY.PLSL.NVDKVLE.PPVVY.RQEQEEE..KRY..Q
Retrocopy ITYTSKHSVEVQVNMMSENILTGAKKLTNKATLWYAPLSLTNVDKVLEEPPVVYFRQEQEEEVQKRYKTQ

Parental  KLERMETKWRNGDIVQPVLNPEPNTVSYSQSSLIHLVGPSDCTLHGFVHGGVTMKLMDEVAGIVAARHCK
          KLERMET.WRNGDIVQPVLNPEPNTVSYSQSSLIHLVGPSDCTLH.F.H.G.TMK.MDEVAGI.AARHCK
Retrocopy KLERMETNWRNGDIVQPVLNPEPNTVSYSQSSLIHLVGPSDCTLHSFMHEGLTMKVMDEVAGILAARHCK

Parental  TNIVTASVDAINFHDKIRKGCVITISGRMTFTSNKSMEIEVLVDADPVVDSSQKRYRAASAFFTYVSLSQ
          TN..TAS..AINF..KIRK.C..TISGRMTFTSNKS.EIEVLVDAD.VVDSSQKRYRAA...FT.VSLSQ
Retrocopy TNLNTASMEAINFDNKIRKVCIKTISGRMTFTSNKSVEIEVLVDADCVVDSSQKRYRAAGV-FT*VSLSQ

Parental  EGRSLPVPQLVPETEDEK
          EGRSLP.PQLVPET.DEK
Retrocopy EGRSLPMPQLVPETQDEK

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	0.14 RPM	133.83 RPM
SRP007412_cerebellum	0.00 RPM	54.85 RPM
SRP007412_heart	0.00 RPM	1.49 RPM
SRP007412_kidney	0.03 RPM	10.28 RPM
SRP007412_liver	0.16 RPM	14.89 RPM
SRP007412_testis	0.00 RPM	11.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2047 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2047 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3034
Pongo abelii	retro_pabe_2513

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000157	2 retrocopies	retro_cjac_1229, retro_cjac_457,
Homo sapiens	ENSG00000097021	1 retrocopy	retro_hsap_3034,
Mustela putorius furo	ENSMPUG00000006882	1 retrocopy	retro_mputfur_177,
Nomascus leucogenys	ENSNLEG00000010371	1 retrocopy	retro_nleu_845,
Pongo abelii	ENSPPYG00000001945	1 retrocopy	retro_pabe_2513,
Pan troglodytes	ENSPTRG00000000084	1 retrocopy	retro_ptro_2047 ,