RetrogeneDB ID: retro_ptro_1938

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:158083347..158084819(-)
• Located in intron of: ENSPTRG00000015549

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX50
• Ensembl ID: ENSPTRG00000002562
• Aliases: None
• Description: None

Sequence

>retro_ptro_1938
AGAAAAGATCTACCAAATGGAAATATTGATGAATATGAAAAAAAAATCAAAGCAAGTATCATCCTTAGATAGTTCTACTC
ATAAATCAAGTGATAATAAACTAGAGGAGACCTTAACATGTGAACAGAAAGAAAGAGCTTTCTCCTATTTCCGTATTTCT
GAAGAGACTGTAAAGCTTCTGAAACATCAAAGGGTAACATATCTCTTTCCTATTCAAGTTAGGACCTTGTCCTGTATATG
AAAGAAAAGATTTAATAGCTCGAGCATGGACAGGAACAGGAAAGACATTCTTTTTTGCCATCCCCTTGGTTGAAAGACTC
CAAAGAAATCAAGAAACAATTTTTAAAAAGCTGCTCAACAAAGGTACTTGTTTTGGCTCCAGCAAGGGAACTGGCAAACC
AAGTAGCCAAAGACTTCAAAGATAAAACTAGGAAACTCAGCATGGTGTGTTTTTATGGTGCAATACCATATCAAAGCCAA
ATTAATCATATGCAAAATGGTATTGACTTCTTGGTTGGAACCCCTGGTCATATCAAAGATCATCTGCAGAGTGGCTGATT
GGATCTTTCTAAACTGCGCCATTTTGTGCTTGATGAAGTGGATCAAACGTTAGATTTAGATTTTAATGAACAAGTTGAAG
ATGTGATTCACAAATCCTACAAAACTGAATCTGAAGACCATCCTCAGACTTTACTTTTTTCTGCAACTTGCCCACAGTGG
GTATACAAAGTTGCAAATAAATACATGAAATCCAGATATGAACAGGTTGACCTTATTGGATAAATGACTCAAAAGGCTGC
AACTACTGTGGAACACTTGGCCATTCAGTGTCATTGGTCTCAGAGGCCAGCAGTTATTGGAGATGTCCTTCAAGTCTACA
GTGGGTCTGAAGGGAGGGCTATTATTTTCTGTGAGACCAGGAAGAATGTAACTGAAATGGCCATGAATCCACACATAAAA
CAGAATGCCCAGTGTTTACATGGGGACATTGCACAGTCACAAAGAGAAATTACACTAAAAGGCTTCAGAGAAGATAGTTT
TAAAGTTTTGGTGGCAACCAATGTGGCTGCCCATAGTTTGCACATTCCTGAAGTAGACCTGGTGATTCAACGTTCTCCTC
CTCAGGATGTTGAGGCCCGTATCCATCGCTCTGGATGCACAGGTAGAGCTGGACAGGGATTTGTATATGTTTTTATCAAC
CAAGAGAAAGAGGTCAACTAAGATATGTGGAACAAAAAGCAAGAATTACTTTTAAATGTGTAGGTGTTCCTTCTACAATG
GATTTAGTTAAATCTAAAAGCATGGATACCATCAGGTTTCTGACTTCCGTTTCTTATGCTGCTGTTGATTTTTTCTGACC
ACCAGCTCAGAGACTGATAGAAGAGAAAGGGGCAGTGGATGCATTGGCTGCAACTTTAGCCCACATTTCTGGCGCATCAA
GTTTTGAACCACAGTCTTTGATCGCCTCTGAT

Alignment

ORF - retro_ptro_1938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.05 %
• Parental protein coverage: 69.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKDLPNGDIDEYEKK-SKRVSSLDTSTHKSSDNKLEETLTREQKEGAFSNFPISEETIKLLKGRGVTYLF
          RKDLPNG.IDEY....SK.VSSLD.STHKSSDNKLEETLT.EQKE.AFS.F.ISEET.KLLK...VTYLF
Retrocopy RKDLPNGNIDEYXXX>SKQVSSLDSSTHKSSDNKLEETLTCEQKERAFSYFRISEETVKLLKHQRVTYLF

Parental  PIQVKTFGPVYEGKDLIAQARTGTGKTFSFAIPL-IERLQRNQETI-KKSRSPKVLVLAPTRELANQVAK
          PIQV.T.......K...........K...F..PL..ERLQRNQETI..KS.S.KVLVLAP.RELANQVAK
Retrocopy PIQVRTLSCI*K-KRFNSSSMDRNRKDILFCHPL>VERLQRNQETI>LKSCSTKVLVLAPARELANQVAK

Parental  DFKDITRKLSVACFYGGTSYQSQINHIRNGIDILVGTPGRIKDHLQSGRLDLSKLRHVVLDEVDQMLDLG
          DFKD.TRKLS..CFYG...YQSQINH..NGID.LVGTPG.IKDHLQSG.LDLSKLRH.VLDEVDQ.LDL.
Retrocopy DFKDKTRKLSMVCFYGAIPYQSQINHMQNGIDFLVGTPGHIKDHLQSG*LDLSKLRHFVLDEVDQTLDLD

Parental  FAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQC
          F.EQVED.IH.SYKT.SED.PQTLLFSATCPQWVYKVA.KYMKSRYEQVDL.G.MTQKAATTVEHLAIQC
Retrocopy FNEQVEDVIHKSYKTESEDHPQTLLFSATCPQWVYKVANKYMKSRYEQVDLIG*MTQKAATTVEHLAIQC

Parental  HWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSF
          HWSQRPAVIGDVLQVYSGSEGRAIIFCET.KNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFRE.SF
Retrocopy HWSQRPAVIGDVLQVYSGSEGRAIIFCETRKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREDSF

Parental  KVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICF-YQPRERGQLRYVEQKAG
          KVLVATNVAA..L.IPEVDLVIQ.SPPQDVE..IHRSG.TGRAG..G....F.YQPRERGQLRYVEQKA.
Retrocopy KVLVATNVAAHSLHIPEVDLVIQRSPPQDVEARIHRSGCTGRAGQ-GFVYVF<YQPRERGQLRYVEQKAR

Parental  ITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSFEPR
          ITFK.VGVPSTMDLVKSKSMD.IR.L.SVSYAAVDFF.P.AQRLIEEKGAVDALAA.LAHISGASSFEP.
Retrocopy ITFKCVGVPSTMDLVKSKSMDTIRFLTSVSYAAVDFF*PPAQRLIEEKGAVDALAATLAHISGASSFEPQ

Parental  SLITSD
          SLI.SD
Retrocopy SLIASD

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	0.04 RPM	18.07 RPM
SRP007412_cerebellum	0.00 RPM	30.83 RPM
SRP007412_heart	0.00 RPM	19.79 RPM
SRP007412_kidney	0.05 RPM	28.17 RPM
SRP007412_liver	0.00 RPM	15.16 RPM
SRP007412_testis	0.00 RPM	55.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1938 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1938 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2866
Pongo abelii	retro_pabe_2369

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298,
Homo sapiens	ENSG00000107625	2 retrocopies	retro_hsap_2089, retro_hsap_2866,
Macaca mulatta	ENSMMUG00000001006	1 retrocopy	retro_mmul_982,
Mus musculus	ENSMUSG00000020076	1 retrocopy	retro_mmus_3362,
Nomascus leucogenys	ENSNLEG00000011631	2 retrocopies	retro_nleu_1300, retro_nleu_609,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938 ,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,