RetrogeneDB ID: retro_ptro_1536

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:32682971..32684091(+)
• Located in intron of: ENSPTRG00000011815

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_1536
TTGGATCTTTCTAAACTGTGCCATGTTGTGCTTGATGAAGTGGATCAAATGTTAGAGTTAGGTTTTGCTGAACAAGTTGA
AGATATTATTCATGAATTCTACAAAACTGATTCTGAAGACAGTCCTCAGACTTTACTTTTTTCTGCAGCTTGCCCACAGT
GGGTATGCAAAGTTGCAAAAAAATGCGTGAAATCCAGATACGAACAGATTGATGTTGTTGGAAAAATGACTCAAAAGGCT
GCAGCTTCTGTGGAACATTTGGCCATCCAGTGTCATTGGTCTCAGAGGCCAGCAGTTACTGGAGATGTCCTTCAAGTCTA
CAGTGGGTCTGAAGGGACGGCTATTATTTTCTGTGAGACCCAGAGGAGTGTAACTGAAATAGCCATGAATCCACACATAA
AACAGAATGCCCAGTGTTTACATGGGGACATTGCACAGTCACAAAGAGAAATTACACTAAAAGACTTCAGAGAAGGTAGT
TTTAAAGTTTTGGTGGCAACCAACGTGGCTGCCCGTGGTTTGGACATTCCTGAAGTTGACCTGGTGATTCATGGTTCTCC
TCCTCAGGATGTTGAGTCTATATCCATCGTTCTGGATGCACAGGTAGAGCTGGACAGACAGGGATTTGTATATGTTTTTA
TCAACCAAGAGAAAGAGGTCAACTAAGATATGTGGAACAAAAAGCAGGAATTACTTTTAAATGTGTAGGTATTCCTTCTA
CAATGGATTTAGTTAAATCTAAAAGCACGGATGCCATAAGGTCTCTGGCTTCTGTTTCTTATGCTGCTGTTGATTTTTTC
CAACCATCAGCTCAGATACTTAGAGAAGAGAAAGGGGCAGTGGATGCACTGGCTGCAGCTTTAGCCCACATTTCTGGTGC
ATCAGGCTTTGAACCACGATCTTTGATCACCTCTGATAGGGATTTGTGACCATGACTCTGGAAAGCCTAGAGGAAATACA
GGATGTCAGCTGTGCTTGGAAAGAACTTAACAGAAAGCTGAGTAGTAATGCAGTGTCTCAGATTACCAGAATGTGCCTCA
TGAAAGGAAATGTGCGTGTTTGCTTTGATGTTCCTACAACTAAGTCAGAAAGGTTACAGGCAGAGTGGCATGATTCCGAC

Alignment

ORF - retro_ptro_1536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 50.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDLSKLRHVVLDEVDQMLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQV
          LDLSKL.HVVLDEVDQML.LGFAEQVEDIIHE.YKTDSED.PQTLLFSA.CPQWV.KVAKK..KSRYEQ.
Retrocopy LDLSKLCHVVLDEVDQMLELGFAEQVEDIIHEFYKTDSEDSPQTLLFSAACPQWVCKVAKKCVKSRYEQI

Parental  DLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCL
          D.VGKMTQKAA..VEHLAIQCHWSQRPAV.GDVLQVYSGSEG.AIIFCET...VTE.AMNPHIKQNAQCL
Retrocopy DVVGKMTQKAAASVEHLAIQCHWSQRPAVTGDVLQVYSGSEGTAIIFCETQRSVTEIAMNPHIKQNAQCL

Parental  HGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVES-YIHRSGRTGRAGRTGI
          HGDIAQSQREITLK.FREGSFKVLVATNVAARGLDIPEVDLVI..SPPQDVES.YIHRSG.TGRAG.TGI
Retrocopy HGDIAQSQREITLKDFREGSFKVLVATNVAARGLDIPEVDLVIHGSPPQDVES<YIHRSGCTGRAGQTGI

Parental  CICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKG
          CICFYQPRERGQLRYVEQKAGITFK.VG.PSTMDLVKSKS.DAIRSLASVSYAAVDFF.PSAQ.L.EEKG
Retrocopy CICFYQPRERGQLRYVEQKAGITFKCVGIPSTMDLVKSKSTDAIRSLASVSYAAVDFFQPSAQILREEKG

Parental  AVDALAAALAHISGASSFEPRSLITSDK-GFVTMTLESLEEIQDVSCAWKELNRKLSSNAVSQITRMCLL
          AVDALAAALAHISGAS.FEPRSLITSD..GFVTMTLESLEEIQDVSCAWKELNRKLSSNAVSQITRMCL.
Retrocopy AVDALAAALAHISGASGFEPRSLITSDR<GFVTMTLESLEEIQDVSCAWKELNRKLSSNAVSQITRMCLM

Parental  KGNMGVCFDVPTTESERLQAEWHDSD
          KGN..VCFDVPTT.SERLQAEWHDSD
Retrocopy KGNVRVCFDVPTTKSERLQAEWHDSD

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	0.20 RPM	18.07 RPM
SRP007412_cerebellum	0.39 RPM	30.83 RPM
SRP007412_heart	0.09 RPM	19.79 RPM
SRP007412_kidney	0.13 RPM	28.17 RPM
SRP007412_liver	0.03 RPM	15.16 RPM
SRP007412_testis	0.11 RPM	55.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1536 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1536 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2089
Pongo abelii	retro_pabe_2007
Macaca mulatta	retro_mmul_982

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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,