RetrogeneDB ID: retro_pabe_2007

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:79824840..79826072(-)
• Located in intron of: ENSPPYG00000012508

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_2007
CTACTTTTTTCTGCAGCTTGCCCACAGTGGGTATGCAAAGTTGCAAAAAAATGTGTGAAATCCAGATACGAACAGATTGA
CGTTGTTGGAAAAATGACTCAAAAGGCTGCAGCTACTGTGGAACATTTGGCCATCCAGTGTCACTGGTCTCAGAGGCCCG
CAGTTATTGGAGATGTCCTTCAAGTCTACAGTGGGTCTGAAGGGAGGGCTATTATTTTGTATGAGACCCAGAGGAGTGTA
ACTGAAATGACCATGAATCCACACCTAAAACAGAATGCCCAGTGTTTACATGGGGACATTGCACAGTCACAAAGAGAATT
TACACTAAAAGGCTTCAGAGAAGGTAGTTTTAAAGTTTTGGTGGCAACCAACATGGCTGCCCGTGGTTTGGACATTCCTG
AAGTTGACCTGGTGATTCAGAGTTCTCCTCCTTAGGATGTTGAGTCTATATCCATCGTTCTGGACACACAGGTAGAGCTG
GACGGACAGGGATTTGTATATGTTTTTATCAACCAAGAGAAAGAGGTCAACTAAGATACGTGGAACAAAAAGCAGAAATT
ACTTTTAAATGTGTAGGTATTCCTTCTACAATGGATTTAGTTAAATCTGAAAGCATGGATGCCATAAGGTCTCTGGCTTC
TGTTTCTTATACTGCTGTTGATTTTTTCCAACCATCAGCTCAGATACTGATAGAAGAGAAAGGGGTAGTGGATGCATTGG
CTGCAGCTTTAGCCCACATTTCTGGTGCATCAAGCTTTGAACCACGATCTTTGATCATCTCTGATAAGGGATTTGTGACC
ATGACTCTGGAAAGTCTGGAGGAAATACAGGATGTCAGCTGTTCTTGGAAAGAACTTAACAGAAAGCTGAGTAGTAATGC
AGTGTCTCAGATTACCAGAATGTGCCTCCTGAAAGGAAATGTGGGTGTTTGCTTTGATGTTCCCACAACTAAGTCAGAAA
GGTTACAGGCAGAGTGGCATGATTCCGACTGGATATTCTCAGTGCCAGCCAAATTACCTGAAATTGAAGAATATTATGAT
GGAAACACATCTAATTCCAGACAGAGGAGTGGTTAGTCAAGTGGCCAGTCGGGCCGATCAAGTGGTCGATCTGGCAGCCG
GTCAGTTAGACAGAGTCCACAAGGGAGTCGCTCAGGAAGTCGACGAGATGGTAGAAGATGAAGAGGGAATAGAAATTGAT
CAAGAAGTGGGAGCCACAAACGGAGTTTTGAC

Alignment

ORF - retro_pabe_2007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRA
          LLFSA.CPQWV.KVAKK..KSRYEQ.D.VGKMTQKAA.TVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRA
Retrocopy LLFSAACPQWVCKVAKKCVKSRYEQIDVVGKMTQKAAATVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRA

Parental  IIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQ
          II..ET...VTEM.MNPH.KQNAQCLHGDIAQSQRE.TLKGFREGSFKVLVATN.AARGLDIPEVDLVIQ
Retrocopy IILYETQRSVTEMTMNPHLKQNAQCLHGDIAQSQREFTLKGFREGSFKVLVATNMAARGLDIPEVDLVIQ

Parental  SSPPQDVES-YIHRSGRTGRAGRTGICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAI
          SSPP.DVES.YIHRSG.TGRAGRTGICICFYQPRERGQLRYVEQKA.ITFK.VG.PSTMDLVKS.SMDAI
Retrocopy SSPP*DVES<YIHRSGHTGRAGRTGICICFYQPRERGQLRYVEQKAEITFKCVGIPSTMDLVKSESMDAI

Parental  RSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSFEPRSLITSDKGFVTMTLESLEEIQDV
          RSLASVSY.AVDFF.PSAQ.LIEEKG.VDALAAALAHISGASSFEPRSLI.SDKGFVTMTLESLEEIQDV
Retrocopy RSLASVSYTAVDFFQPSAQILIEEKGVVDALAAALAHISGASSFEPRSLIISDKGFVTMTLESLEEIQDV

Parental  SCAWKELNRKLSSNAVSQITRMCLLKGNMGVCFDVPTTESERLQAEWHDSDWILSVPAKLPEIEEYYDGN
          SC.WKELNRKLSSNAVSQITRMCLLKGN.GVCFDVPTT.SERLQAEWHDSDWI.SVPAKLPEIEEYYDGN
Retrocopy SCSWKELNRKLSSNAVSQITRMCLLKGNVGVCFDVPTTKSERLQAEWHDSDWIFSVPAKLPEIEEYYDGN

Parental  TSSNSRQRSGWSSGRSGRSGRSGGRSGGRSGRQSRQGSRSGSRQDGRRRSGNRNRSRSGGHKRSFD
          T.SNSRQRSG.SSG.SGRS....GRSG.RS.RQS.QGSRSGSR.DGRR..GNRN.SRSG.HKRSFD
Retrocopy T-SNSRQRSG*SSGQSGRS---SGRSGSRSVRQSPQGSRSGSRRDGRR*RGNRN*SRSGSHKRSFD

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	0.39 RPM	24.94 RPM
SRP007412_cerebellum	0.49 RPM	36.72 RPM
SRP007412_heart	0.21 RPM	16.20 RPM
SRP007412_kidney	0.53 RPM	25.39 RPM
SRP007412_liver	0.43 RPM	20.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2007 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2007 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2089
Pan troglodytes	retro_ptro_1536
Macaca mulatta	retro_mmul_982

---

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,