RetrogeneDB ID: retro_pabe_1653

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:59220170..59221482(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD3
• Ensembl ID: ENSPPYG00000012216
• Aliases: PTCD3, MRP-S39
• Description: pentatricopeptide repeat-containing protein 3, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001126041]

Sequence

>retro_pabe_1653
ATGGCAGCTGTAGCTGCTGTTCACTGGCTGGGGCTCTGCAGCAGGCTTGACCAGCCATTGACGGGTCAGCCGGCAGGTCT
GTGTGAACAGGCACATAGCTGCAGATTTTATTCTGGAAGTGCAACCCTCTCAAATATTGAAGGAACTGATATAACAGGGA
TTGAAGCAGTAGTAATTCCAAAAAAGAAAACTTGGGATAAAGTAGCCATTCTTCAGGCTCTTGCATTCACAGTAAACAGG
GTTCCCATGGCTGTACCTAGCGCATTTCAAGATAATCCTTACCTCATACCAACATCCTCTTCAGAATCTCGTTCATTTTT
ACTGGCAAAGAAATCTGGGGAGAATATGGCCAAGGTCATTATTAATTCATACACCAAATATTTTCAGAAGGACATAGCTG
AACCTCATATACTATGTTTAATGCCTGAGTACTTTGAACCTCAGATCAAAGACATAAGTGAAGCCACCCTCAAGGAACGA
ATCAAGCTCAGATAAGTCAAAGCCTCTGTGGACATGTTTGATCAGCTTTTGCAAGCAGGAACCACGGTGTCTCTTGGAAC
AACATATAGTCTCTCAGATTTATTGTGTTACTATGGTGACCAGGAGCCCTCAACTGATTATCATTTTCAACAAACTGAAC
AGTCAAAAGAATTGGAAGAGGAAAATAATAAGCGGTCTAGGAGGAAAGCTGGTCATCAGTTTGGAGTTACCTGGTGAGCA
AAAAATAACGCTGAGAGAATCTTTTCTCTGATGCCAGAGAAAAATGCACATTCCTATTGCACAGTGATCCGAGGAATGGT
GAAGCACCAAGCTTATGAGCAGGCATTAAACCTGTACACTGAGTTACTAAACAACAGACTCTGTGCTGGTGTATACACAT
TTAATGCAGTGATTGAAGCAACAGTATTGGTGATAAATAAGAAATTTGAGGAAGAATGGAATAATATACTGGAGCTGCTA
AGACAAATGGTTGCACAGAAGGTGAAACCAAATCTACAGACTTTTAATACCATTCTGAAATGTCTCTGAAGATTTTATGT
ACTTGCAGGATTGCCAGCCTTACAGATTCTACGTGAAATGAAAGCCATCAGAATAGAACCCTCGCTTGCAACATATCACC
ATATTATTCAGCTGTTTTATCAGCCTGGAAGCCCTTCAAAGGGATCATCTTTCATCATCTATGATATAATGAATGAATTA
AAGGGAAAGAGATTTTCCTCCAAAGGACCTGGATGATGATAAGTTTTTTCAGTCAGCCATGAGAGTATCCTCATCTCTCA
GAGATCTAGAACTTGCCTAGCAAATACACGGC

Alignment

ORF - retro_pabe_1653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.88 %
• Parental protein coverage: 63.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGVSAVRWLGLRSRLGQPLTGRRAGLCKQARSCRFYSGSATLSKVEGTDITGIEEVVIPKKKTWDKVAV
          MA.V.AV.WLGL.SRL.QPLTG..AGLC.QA.SCRFYSGSATLS..EGTDITGIE.VVIPKKKTWDKVA.
Retrocopy MAAVAAVHWLGLCSRLDQPLTGQPAGLCEQAHSCRFYSGSATLSNIEGTDITGIEAVVIPKKKTWDKVAI

Parental  LQALASTVNRDTTSVPYVFQDDPYLIPASSLESRLFLLAKKSGENVAKFIINSYPKYFQKDIAEPHIPCL
          LQALA.TVNR....VP..FQD.PYLIP.SS.ESR.FLLAKKSGEN.AK.IINSY.KYFQKDIAEPHI.CL
Retrocopy LQALAFTVNRVPMAVPSAFQDNPYLIPTSSSESRSFLLAKKSGENMAKVIINSYTKYFQKDIAEPHILCL

Parental  MPEYFEPQIKDISEAALKERIELRKVKASVDMFDQLLQAGTTVSLETTNSLLDLLCYFGDQEPSTDYHFQ
          MPEYFEPQIKDISEA.LKERI.LR.VKASVDMFDQLLQAGTTVSL.TT.SL.DLLCY.GDQEPSTDYHFQ
Retrocopy MPEYFEPQIKDISEATLKERIKLR*VKASVDMFDQLLQAGTTVSLGTTYSLSDLLCYYGDQEPSTDYHFQ

Parental  QTEQSEALEVENDETSRRKAGHQFGVTWQAKNNAERIFSLMPEKNAHSYCTMIRGMVKHRAYEQALNLYT
          QTEQS..LE.EN...SRRKAGHQFGVTW.AKNNAERIFSLMPEKNAHSYCT.IRGMVKH.AYEQALNLYT
Retrocopy QTEQSKELEEENNKRSRRKAGHQFGVTW*AKNNAERIFSLMPEKNAHSYCTVIRGMVKHQAYEQALNLYT

Parental  ELLNNRLHADVYTFNALTEATVCVINEKFEEKWSKIQELLRHMVAQKVKPNLQTFNTILKCLRRFHVFAR
          ELLNNRL.A.VYTFNA..EATV.VIN.KFEE.W..I.ELLR.MVAQKVKPNLQTFNTILKCL.RF.V.A.
Retrocopy ELLNNRLCAGVYTFNAVIEATVLVINKKFEEEWNNILELLRQMVAQKVKPNLQTFNTILKCL*RFYVLAG

Parental  SPALQILREMKAIGIEPSLATYHHIIHVFDQPGDPLKRSSFIIYDIMNELMGKRFS-PKDPDDDKFFQSA
          .PALQILREMKAI.IEPSLATYHHII..F.QPG.P.K.SSFIIYDIMNEL.GKRFS.PKD.DDDKFFQSA
Retrocopy LPALQILREMKAIRIEPSLATYHHIIQLFYQPGSPSKGSSFIIYDIMNELKGKRFS>PKDLDDDKFFQSA

Parental  MSICSSLRDLELAYQVHG
          M...SSLRDLELA.Q.HG
Retrocopy MRVSSSLRDLELA*QIHG

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	54.85 RPM
SRP007412_cerebellum	0.00 RPM	132.42 RPM
SRP007412_heart	0.00 RPM	65.75 RPM
SRP007412_kidney	0.00 RPM	82.44 RPM
SRP007412_liver	0.03 RPM	80.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1653 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1653 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2017
Gorilla gorilla	retro_ggor_1461

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132300	1 retrocopy	retro_hsap_2017,
Gorilla gorilla	ENSGGOG00000001793	1 retrocopy	retro_ggor_1461,
Nomascus leucogenys	ENSNLEG00000002493	1 retrocopy	retro_nleu_2729,
Pongo abelii	ENSPPYG00000012216	1 retrocopy	retro_pabe_1653 ,