RetrogeneDB ID: retro_ptro_1373

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:45206432..45207861(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PATL1
• Ensembl ID: ENSPTRG00000003697
• Aliases: None
• Description: None

Sequence

>retro_ptro_1373
AAGATTCTGCGTTCAAAGCCTGTCCATGTTCGGCCCCCAATGCCACCGTGTTATCCTGGTCCCTATGATGAGAGGATGCC
TCCAAATCAGCTCTACAGTGTCCTGAACTCTTCCTTCCTGGGTCACCCTTTTCCTCCTAGTGTTCCTCCTGTTCTCAGCC
CCCTTTAGAGAGCACAGCTTCTTGGAGGAGCACAGCTACAGCCTGGACAGATGTCTCCCAGCCAGTTTGCATGGGTCCCT
GGATTTGTTGGTAGTCCACATGCTGCTATGAATCCCAAGTTGCTACAAGGGCAAGTTGGGCAGATGCTTCCCCCAGCACC
AGGCTTCCATGCCTTCTTTAGTGCTCCACCCTCTGCTACACCACCTCCACAGCAGTGCCCTCCTGGCCCAGGACCTCACT
TGCAAAACTTAAGATCTCAAGTCCCAGTGTTTAGACTGGACGCAACTCCCCTCCATCCACAGCACCATTGACTCTTGCAT
CAGAGACAGCAACAGAATAGAAATCAGCATCAGAATCTCAGTGGTGCAGGAGATAGAGGAAGTCACTGGAGCAGTCATCA
AGATCATCTCCGAAAGGATCCATATGCCAGTCTCATGTTGCTGTGGGAAAAGGATTGGGCCTCTAAAATTCAGATGATGC
AACTGCAAAGCAATGATCCCCACCTGGATGATTTTTATTACCAGAATTACTTTGAAAAACTGGAGAAACCATCAGCTGCT
GAAGAAATACGAGGTGATGGCCCTAAAAAGGAGCATAACAAGCTTATTACCCCTCAAGTGGCCAAACTGGAGTGCACCTA
TAAGCCAGTACAATTTGTGGGCTCTTTGGGAAAGCTTACTGTTTCTAGTGTGAATAATCCCTGAAAAATGATTGATGCTG
TTGTGACATCTTGGAGTGAGGATGATGAGATAAAAGAAAAACAAATTCGAGACAAGAGGAGAAAAACCCGTCATAATTAA
GAAAACCTACAGTTTACTCCTTGATGTGGAGGACTATGAAAGACGTTATCTCCTAAGTCTAAGACAGCGACCTGCTCTAA
TGGATGAGCGAAAGTACGGATTTTGTAGCATGTATGACAACTTAAGAGGGAAACAGCCTGGACAAGAGAGGCCTAGTGAT
GACCGCTTTGTACAGATCATGTGTATCCAAAAAGGGAAGACAATGGTTGCCCGTATTCTTCCTTTCCTCTCCACAGAGCA
AGCAGCTGACATTTTCATGACAACAGCCAGGGACCTCCCTTTCCTTATCAAGAAAGATGCACAAGATGAGGTGCTGCCAT
GTTTACTGAGTCCCTTCTCTCTCCTCCTCTATCATCTTCCAACAGTGACTATCACCAGCCTTTTGCAACAGCTAATGAAC
CTACCTCAAAGTGCAGCTACACCAGCTCCCTCCAATCCTCACTTCACTGCTGTGCTCCAGAACAAATTC

Alignment

ORF - retro_ptro_1373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 62.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QILCPKPVHVRPPMPPRYPAPYGERMSPNQLCSVPNSSLLGHPFPPSVPPVLSPLQRAQLLGGAQLQPGR
          .IL..KPVHVRPPMPP.YP.PY.ERM.PNQL.SV.NSS.LGHPFPPSVPPVLSPL.RAQLLGGAQLQPG.
Retrocopy KILRSKPVHVRPPMPPCYPGPYDERMPPNQLYSVLNSSFLGHPFPPSVPPVLSPL*RAQLLGGAQLQPGQ

Parental  MSPSQFARVPGFVGSPLAAMNPKLLQGRVGQMLPPAPGFRAFFSAPPSTAPPPQQHPPGPGPHLQNLRSQ
          MSPSQFA.VPGFVGSP.AAMNPKLLQG.VGQMLPPAPGF.AFFSAPPS..PPPQQ.PPGPGPHLQNLRSQ
Retrocopy MSPSQFAWVPGFVGSPHAAMNPKLLQGQVGQMLPPAPGFHAFFSAPPSATPPPQQCPPGPGPHLQNLRSQ

Parental  APMFRPDTTHLHPQHRRLLHQRQQQNRNQHRNLNGAGDRGSHRSSHQDHLRKDPYANLMLQREKDWVSKI
          .P.FR.D.T.LHPQH..LLHQRQQQNRNQH.NL.GAGDRGSH.SSHQDHLRKDPYA.LML..EKDW.SKI
Retrocopy VPVFRLDATPLHPQHH*LLHQRQQQNRNQHQNLSGAGDRGSHWSSHQDHLRKDPYASLMLLWEKDWASKI

Parental  QMMQLQSTDPYLDDFYYQNYFEKLEKLSAAEEIQGDGPKKERTKLITPQVAKLEHAYKPVQFEGSLGKLT
          QMMQLQS.DP.LDDFYYQNYFEKLEK.SAAEEI.GDGPKKE..KLITPQVAKLE..YKPVQF.GSLGKLT
Retrocopy QMMQLQSNDPHLDDFYYQNYFEKLEKPSAAEEIRGDGPKKEHNKLITPQVAKLECTYKPVQFVGSLGKLT

Parental  VSSVNNPRKMIDAVVTSRSEDDETKEKQVRDKRRKT-LVIIEKTYSLLLDVEDYERRYLLSLEEERPALM
          VSSVNNP.KMIDAVVTS.SEDDE.KEKQ.RDKRRKT...I..KTYSLLLDVEDYERRYLLSL...RPALM
Retrocopy VSSVNNP*KMIDAVVTSWSEDDEIKEKQIRDKRRKT>VII-KKTYSLLLDVEDYERRYLLSL-RQRPALM

Parental  DDRKHKICSMYDNLRGKLPGQERPSDDHFVQIMCIRKGKRMVARILPFLSTEQAADILMTTARNLPFLIK
          D.RK...CSMYDNLRGK.PGQERPSDD.FVQIMCI.KGK.MVARILPFLSTEQAADI.MTTAR.LPFLIK
Retrocopy DERKYGFCSMYDNLRGKQPGQERPSDDRFVQIMCIQKGKTMVARILPFLSTEQAADIFMTTARDLPFLIK

Parental  KDAQDEVLPCLLSPFSLLLYHLPSVSITSLLRQLMNLPQSAATPAPSNPHLTAVLQNKF
          KDAQDEVLPCLLSPFSLLLYHLP.V.ITSLL.QLMNLPQSAATPAPSNPH.TAVLQNKF
Retrocopy KDAQDEVLPCLLSPFSLLLYHLPTVTITSLLQQLMNLPQSAATPAPSNPHFTAVLQNKF

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	2.56 RPM	18.55 RPM
SRP007412_cerebellum	1.94 RPM	47.54 RPM
SRP007412_heart	0.35 RPM	36.20 RPM
SRP007412_kidney	0.81 RPM	53.95 RPM
SRP007412_liver	0.07 RPM	62.75 RPM
SRP007412_testis	2.95 RPM	85.57 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1373 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1373 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2059

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166889	1 retrocopy	retro_hsap_2059,
Pan troglodytes	ENSPTRG00000003697	1 retrocopy	retro_ptro_1373 ,