RetrogeneDB ID: retro_ptro_1003

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:33456618..33458623(+)
• Located in intron of: ENSPTRG00000006899

Retrocopy information

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

Parental gene information

• Parental gene symbol: LARP4
• Ensembl ID: ENSPTRG00000004935
• Aliases: None
• Description: La ribonucleoprotein domain family, member 4 [Source:UniProtKB/TrEMBL;Acc:K7ANC5]

Sequence

>retro_ptro_1003
AATGCAGAGCTCTCAGAAGATATATGTAAAGAATATGAAGTAATGTGTTCTTTGTCTTGTGAAACCACAAGAAATACTAC
AGGCATTGAAGAATCAACTGATGGGATGATTTTAGGACCAGAAGATCTGAGTTACCAAATATATGATGTTTCTGGAGAAA
GCAATTCAGCAATTTCTACAGAAGACCTAAAAGAATGTCTAAAGAAACAATTAGAATTCTGGTTTTCACGAGAAAATTTG
TCAAAGGATCTTTACTTGATCTCTCAAATGGATAGTGATCAGTTCATCCCAATTTGGACAGTTGTTAACATGGAAGAAAT
AAAAAAGTTGACCACAGACCCTGATGTAATTCTTGAAGTGTTAAGTTCTTCTCCCATGGTACAAATTGATGAGAAGGGTA
AAAAAGTGAGCCAAGTCATAAGCGTTGTATTGTGATTCTTAGAGAGATTCCTGAAACAACACCAATAGAGGAAGTGAAAG
CTTTGTTCAAATTGAAAACTGCCCCAAAGTGATAAGTTGTGAGTTTGCACACAGTAGCAGCTGGTATATCACTTTCCAGT
CAGACACAGATGCACAAAAGGCTTTTAAATCCTTAAGAGAAGAAGTTAAAACATTTCAGGGCAAGCCAATTATGGCAAGG
ATAAAAGCCATCAATACATTTTTTGCTAAGAATTGTTACTAATTAATGGATTCTAGTATCTATAGTTAGCCCATTCAGAC
TCAAGCACAGTATGCCTCCCCAGTCTTTGTGCAGCCTGTATATAATCCTCACCAGCAGTTCTCAGTGTATAGTATTATTC
CTCAGTCTTGGTCTCCAAATCCTACACCTTACTTTGAAACACCACTGGCCCACTTTCCCAATGGTAGTTTTGTGAACGGC
ATTAATTCACCAGGATCTTATAAAAGACATGCTACTGCTATGAATACGGGTCGACCATTCCAAAAAAAAAAACCTGAAGC
CTCATTTTAGGTCATCCAGTGGTTCAGAACACTCAACAGAGGACTCTGTATCATTGGGGGATGGACAATTGAACAGATCT
AGTTCAAAAAATTTTTCAACTGAAAGCATAATCCTACAGTAACTGGGGATTAGGAGCAAACTTAACTTCAAAAGGAGACT
TCCACTTTGCAGATGGAACAAAATGGGGACTATGGTAGGGGCAGGAGAACTCTTTTCAAAGGTCGAAGATGACGACAAGA
TGTCAATCTCAAGACCTCATCCTTCAACAGCTGAATCAAAGCCTCCAACACCAAAGTTTGACTTACTAGCCTCAAATTTT
CCACCTTTACCTGGAAGTTCATCAAGAATCCCAGATAAACTCATTTTGGAGAATAGGATGTCTGATGTTGTTAAAGGTGT
CTACAAAGAAAAGGATAATGAAGTGTTGAGAGTTAGTTGCCCAGTGCCTGCAGATGAACAGACAGAATGCACTTCTGCCC
AGCAACTCAGTATGAGTACCAGTTCTCCATGTGCAGCTGAGCCTACTGCATTAAGCACAACTCAGCCAAAAAAAAAAAAG
GATCTAATAGAGGATTCCTCTGTTCAGAAGGATGGTCTCAACCAGACGACTATACCAGTTTCTCCTCCAAGTACTACAAA
GCCATGGAGGGCAAGTACTGCCTCACCATGTAATAGTAACATAAATGTAGCTACACCGTGACTCTACAGGAACCCTGAAA
GTTAAGTTATGCTGAAGTGTGCCAGAAGCCCCCTAAAGAGCCATCTTCAGTTCTTGTGTAGCCACTATGGGAACTTTGCT
CCAATGTAGTGTCTCCCACCACAAACAAAGACAATGAAGCTCCTTAGAAGTCCCTTGAGAAACCAAATGAGAAGCCAGAA
GCAAGGGCTAGTAAGGATTATTCTGGCTTCTGAGGCCATACCATTCCCAGGGGAGCAGCTGGAAAAATCAGGGAACAGAG
ATGCCAGTTTAGTCATAGGGCTATACCTCAGGGAGTGACATGACGTAATGGCAAAGAGCAATATGTGCCACCCAGATCAC
CAAAG

Alignment

ORF - retro_ptro_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 91.51 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NAELSEDICKEYEVMYSSSCETTRNSTGIEESTDGMILGPEDLSYQIYDVSGESNSAVSTEDLKECLKKQ
          NAELSEDICKEYEVM.S.SCETTRN.TGIEESTDGMILGPEDLSYQIYDVSGESNSA.STEDLKECLKKQ
Retrocopy NAELSEDICKEYEVMCSLSCETTRNTTGIEESTDGMILGPEDLSYQIYDVSGESNSAISTEDLKECLKKQ

Parental  LEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEKV-RPS
          LEF.FSRENLSKDLYLISQMDSDQFIPIWTV.NMEEIKKLTTDPD.ILEVL.SSPMVQ.DEKG.KV..PS
Retrocopy LEFWFSRENLSKDLYLISQMDSDQFIPIWTVVNMEEIKKLTTDPDVILEVLSSSPMVQIDEKGKKV<EPS

Parental  HKRCIVILREIPETTPIEEVKALFKS-ENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQG
          HKRCIVILREIPETTPIEEVKALFK..ENCPKVISCEFAH.S.WYITFQSDTDAQ.AFK.LREEVKTFQG
Retrocopy HKRCIVILREIPETTPIEEVKALFKL<ENCPKVISCEFAHSSSWYITFQSDTDAQKAFKSLREEVKTFQG

Parental  KPIMARIKAINTFFAKNGYRLMDSSIYSHPIQTQAQYASPVFMQPVYNPHQQYSVYSIVPQSWSPNPTPY
          KPIMARIKAINTFFAKN.Y.LMDSSIYS.PIQTQAQYASPVF.QPVYNPHQQ.SVYSI.PQSWSPNPTPY
Retrocopy KPIMARIKAINTFFAKNCY*LMDSSIYS*PIQTQAQYASPVFVQPVYNPHQQFSVYSIIPQSWSPNPTPY

Parental  FETPLAPFPNGSFVNGFNSPGSYKTNAAAMNMGRPFQKNR-VKPQFRSSGGSEHSTEGSVSLGDGQLNRS
          FETPLA.FPNGSFVNG.NSPGSYK..A.AMN.GRPF......KP.FRSS.GSEHSTE.SVSLGDGQLNRS
Retrocopy FETPLAHFPNGSFVNGINSPGSYKRHATAMNTGRPFXXXX>LKPHFRSSSGSEHSTEDSVSLGDGQLNRS

Parental  SSRNFPTE-RHNPTVTGHQEQTYLQKETSTLQVEQNGDYGRGRRTLFRGRRRREDD-RISRPHPSTAESK
          SS.NF.TE..HNPTVTG..EQT.LQKETSTLQ.EQNGDYGRGRRTLF.G.RR...D..ISRPHPSTAESK
Retrocopy SSKNFSTE<KHNPTVTGD*EQT*LQKETSTLQMEQNGDYGRGRRTLFKG-RR*RQD>SISRPHPSTAESK

Parental  APTPKFDLLASNFPPLPGSSSRMPGELVLENRMSDVVKGVYKEKDNEELTISCPVPADEQTECTSAQQLN
          .PTPKFDLLASNFPPLPGSSSR.P..L.LENRMSDVVKGVYKEKDNE.L..SCPVPADEQTECTSAQQL.
Retrocopy PPTPKFDLLASNFPPLPGSSSRIPDKLILENRMSDVVKGVYKEKDNEVLRVSCPVPADEQTECTSAQQLS

Parental  MSTSSPCAAELTALSTTQQEK--DLIQDSSVQKDGLNQTTIPVSPPSTTKPSRASTASPCNNNINAAT-A
          MSTSSPCAAE.TALSTTQ.....DLI.DSSVQKDGLNQTTIPVSPPSTTKP.RASTASPCN.NIN.AT..
Retrocopy MSTSSPCAAEPTALSTTQXXXXXDLIEDSSVQKDGLNQTTIPVSPPSTTKPWRASTASPCNSNINVAT<T

Parental  VALQEPRKLSYAEVCQKPPKEPSSVLVQPLRELRSNVVSPTKNEDNGAPENSVEKPHEKPEARASKDYSG
          V.LQEP.KLSYAEVCQKPPKEPSSVLV.PL.EL.SNVVSPT.N.DN.AP..S.EKP.EKPEARASKDYSG
Retrocopy VTLQEP*KLSYAEVCQKPPKEPSSVLV*PLWELCSNVVSPTTNKDNEAP*KSLEKPNEKPEARASKDYSG

Parental  FRGNTIPRGAAGKIREQRRQFSHRAIPQGVTRRNGKEQYVPPRSPK
          F.G.TIPRGAAGKIREQR.QFSHRAIPQGVT.RNGKEQYVPPRSPK
Retrocopy F*GHTIPRGAAGKIREQRCQFSHRAIPQGVT*RNGKEQYVPPRSPK

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	0.02 RPM	13.55 RPM
SRP007412_cerebellum	0.04 RPM	19.25 RPM
SRP007412_heart	0.09 RPM	53.37 RPM
SRP007412_kidney	0.05 RPM	56.80 RPM
SRP007412_liver	0.00 RPM	42.00 RPM
SRP007412_testis	0.00 RPM	38.04 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1003 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1003 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1483

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000161813	1 retrocopy	retro_hsap_1483,
Myotis lucifugus	ENSMLUG00000012513	1 retrocopy	retro_mluc_1180,
Macaca mulatta	ENSMMUG00000008172	1 retrocopy	retro_mmul_2129,
Mus musculus	ENSMUSG00000023025	1 retrocopy	retro_mmus_3568,
Nomascus leucogenys	ENSNLEG00000017798	1 retrocopy	retro_nleu_2388,
Pan troglodytes	ENSPTRG00000004935	1 retrocopy	retro_ptro_1003 ,
Rattus norvegicus	ENSRNOG00000049091	1 retrocopy	retro_rnor_644,