RetrogeneDB ID: retro_pabe_2369

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:157412443..157413686(-)
• Located in intron of: ENSPPYG00000014223

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX50
• Ensembl ID: ENSPPYG00000002390
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 50 [Source:HGNC Symbol;Acc:17906]

Sequence

>retro_pabe_2369
CCTGTTTATGAAGGAAAAGATTTAATAGCTCGAGCATGGACAGGAACAGGAAAGTCATTATTTTTTGCCATCCCCTTGAC
TGAAAGACTCCAAAGACATCAAGAAACAATTTTTTAAAAAGCTGCTCACCAAAGGTACTTGTTTTGTCTCCAACAAGGGA
ACTGGCAAACCAAGTAGCCAAAGACTTCAAAGATAAAACTAGGAAACTCAGCATGGCATGTTTTTATGGTGGAACACCAT
ATCAAAGCCAAATTAATCATATGCGAAATGGTATTGACATCTTGGATGGAACTCCTGGTCATATCAAAGATCGTCTGCAG
AGTGGCTGACTGGATCTTTCTAAACTGCGCCTTGTTGTGTTTGATGAAGTGGATCAAATGTTAGATTTAGATTTTGATGA
ACAAGTTGAAGATATGATTTACAAATCTTACAAAACTGATTCTGAAGACAATCCTCAGACTTTACTTTTTTCTGCAACTT
GCCCACAGTGGGTATACAAAGTTGCCAAAAAATACATGAAACCCAGATATGAACAGGTTGACCTTGTTGGAAAAATGACT
CAAAAGGCTGCAACTACTGTGGAACACTTGGTCATTCAGTGTCATTGGTCTCAGAGGCCAGCAGTTATTGGAGATGTCCT
TCAAGTCTACAGTGGGTCTGAAGGGAGGGCTATTATTTTCTGTGAGACCAAGAAGAATGTAACTGAAATGGTCATGAATC
CACACATAAAACAGAATGCCCAGTGTTTACATGGGGACATTGCACAGTCAGAAAGAGAAATTACACTAAAAGGCTTCAGA
GAAGATAGTTTTAAAGTTTTGATGGCAACCAATGTGGCTGCCCATAGTTTGCACATACCTGAAGTAGACCTGGTGATTCA
ACGTTCTCCTCCTCAGGATGTTGAGGCCTGTATCCATCGCTCTGGATGCACAGGTAGAGCTGGACAGGGATTTGTGTATG
TTTTTATCAACCAAGAGAAAGAGGTCAACTAAGATATGTGGAACAAAAAGCAGGAATTACTTTTAAATGTGTAGGTGTTC
CTTCTACAATGGATTTAGTTAAATCTAAAAGCATGGATACCATCAGGTTTCTGACTTCCGTTTCTTATGCTGCTGTTGAT
TTTTTCTGACCATCAGCTCAGAGACTGATGGAAGAGAAAGGGGCAGTGGATGCATTGGCTGCAACTTTAGCCCACATTTC
TGGTGCATCAACTTTTGAACCACGATCTTTGATCGCCTCTGAT

Alignment

ORF - retro_pabe_2369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.97 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVYEGKDLIAQARTGTG-KTFSFAIPLIERLQR-NQETIKKSRSPKVLVLAPTRELANQVAKDFKDITRK
          PVYEGKDLIA.A.TGTG.K...F..PL.............KS.SPKVLVL.PTRELANQVAKDFKD.TRK
Retrocopy PVYEGKDLIARAWTGTG<KVIIFCHPLD*KTPKTSRNNFLKSCSPKVLVLSPTRELANQVAKDFKDKTRK

Parental  LSVACFYGGTSYQSQINHIRNGIDILVGTPGRIKDHLQSGRLDLSKLRHVVLDEVDQMLDLGFAEQVEDI
          LS.ACFYGGT.YQSQINH.RNGIDIL.GTPG.IKD.LQSG.LDLSKLR.VV.DEVDQMLDL.F.EQVED.
Retrocopy LSMACFYGGTPYQSQINHMRNGIDILDGTPGHIKDRLQSG*LDLSKLRLVVFDEVDQMLDLDFDEQVEDM

Parental  IHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAV
          I..SYKTDSEDNPQTLLFSATCPQWVYKVAKKYMK.RYEQVDLVGKMTQKAATTVEHL.IQCHWSQRPAV
Retrocopy IYKSYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKPRYEQVDLVGKMTQKAATTVEHLVIQCHWSQRPAV

Parental  IGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNV
          IGDVLQVYSGSEGRAIIFCETKKNVTEM.MNPHIKQNAQCLHGDIAQS.REITLKGFRE.SFKVL.ATNV
Retrocopy IGDVLQVYSGSEGRAIIFCETKKNVTEMVMNPHIKQNAQCLHGDIAQSEREITLKGFREDSFKVLMATNV

Parental  AARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICICF-YQPRERGQLRYVEQKAGITFKRVGV
          AA..L.IPEVDLVIQ.SPPQDVE..IHRSG.TGRAG..G....F.YQPRERGQLRYVEQKAGITFK.VGV
Retrocopy AAHSLHIPEVDLVIQRSPPQDVEACIHRSGCTGRAGQ-GFVYVF<YQPRERGQLRYVEQKAGITFKCVGV

Parental  PSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSFEPRSLITSD
          PSTMDLVKSKSMD.IR.L.SVSYAAVDFF.PSAQRL.EEKGAVDALAA.LAHISGAS.FEPRSLI.SD
Retrocopy PSTMDLVKSKSMDTIRFLTSVSYAAVDFF*PSAQRLMEEKGAVDALAATLAHISGASTFEPRSLIASD

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	24.94 RPM
SRP007412_cerebellum	0.00 RPM	36.72 RPM
SRP007412_heart	0.00 RPM	16.20 RPM
SRP007412_kidney	0.00 RPM	25.39 RPM
SRP007412_liver	0.00 RPM	20.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2369 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2369 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2866
Pan troglodytes	retro_ptro_1938

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 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	ENSPPYG00000002389	1 retrocopy	retro_pabe_3816,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369 , retro_pabe_2418,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938,