RetrogeneDB ID: retro_pabe_3452

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:21956870..21957537(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARRDC3
• Ensembl ID: ENSPPYG00000015628
• Aliases: None
• Description: arrestin domain-containing protein 3 [Source:RefSeq peptide;Acc:NP_001127608]

Sequence

>retro_pabe_3452
ACTGGCAAAATCAGAGTAAAAGCTCTTAAAATTCATGCAAGAGGACACTTGGAAATACGCTCTGTTGAATCTAGAAACAC
TGACGCCAATACTGCCTGTAGATGGAATTACGTGGAAGAAGTACAATATATCAACCATAAAGATATCTTAATTGGACACA
AAAGAGTCAACGATAATTCCAAAGAAGGCTTCAACACTATTCATTCAGGAAGGCTGAATATGCTTTCAGCTCTGAGCTTC
CAGAGACACCACTTGCTACCTCATTCAAAGGCAGTCGTGGTGTGTGCACTCTTGTGTGAAAGCTGAATCTCAAAAGTCCC
TGACTACTAACAGTAACATCACAGAAGGAATTTACAGTCTCTGAGTATATAAATATGAATACTCCTTCATCGCTGTCACC
CCAAGCAGGCACAGAAGAAAAGACACTAGGTTGCTGGTTTTCTACCTCAGGCTCAATATCCTTAAGTGCCAAAATTGAAA
AGAAGGGCTATACCATGGGTGAATCAACTCAGAAATTTGCTGAGACTGAGAACTGCTCTTTCCAAATGCTAGTGCCAAAG
TCAGCCATTACCAAACACGGGCCTTCCATGCCAAACGGAAGATGAAGGAAGTGAAACAGCATGTGGCTAACTTGCATGAG
GAATCCTTGTCATCTGGAAAGAGAGAC

Alignment

ORF - retro_pabe_3452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.44 %
• Parental protein coverage: 53.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGEIRVKSLKIHARGHAKVRWTESRNAGSNTAYTQNYTEEVEYFNHKDILIGHERDDDNSEEGFHTIHSG
          TG.IRVK.LKIHARGH...R..ESRN...NTA...NY.EEV.Y.NHKDILIGH.R..DNS.EGF.TIHSG
Retrocopy TGKIRVKALKIHARGHLEIRSVESRNTDANTACRWNYVEEVQYINHKDILIGHKRVNDNSKEGFNTIHSG

Parental  R-HEYAFSFELPQTPLATSFEGRHGSVRYWVKAELHRPWLLPVKLKKEFTVFEHIDINTP-LLSPQAGTK
          R..EYAFS.ELP.TPLATSF.G..G......K..L..P.LL.V...KEFTV.E.I..NTP..LSPQAGT.
Retrocopy R<AEYAFSSELPETPLATSFKGSRGVCTLV*KLNLKSP*LLTVTSQKEFTVSEYINMNTPSSLSPQAGTE

Parental  EKTLCCWFCTSGPISLSAKIERKGYTPGESIQIFAEIENCSSRMVVPKAAI-YQTQAFYAKGKMKEVKQL
          EKTL.CWF.TSG.ISLSAKIE.KGYT.GES.Q.FAE.ENCS..M.VPK.AI.YQT.AF.AK.KMKEVKQ.
Retrocopy EKTLGCWFSTSGSISLSAKIEKKGYTMGESTQKFAETENCSFQMLVPKSAI<YQTRAFHAKRKMKEVKQH

Parental  VANLRGESLSSGKTE
          VANL..ESLSSGK..
Retrocopy VANLHEESLSSGKRD

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	27.15 RPM
SRP007412_cerebellum	0.00 RPM	64.21 RPM
SRP007412_heart	0.00 RPM	33.96 RPM
SRP007412_kidney	0.00 RPM	50.75 RPM
SRP007412_liver	0.00 RPM	42.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3452 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3452 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010525	1 retrocopy	retro_cjac_560,
Nomascus leucogenys	ENSNLEG00000013887	1 retrocopy	retro_nleu_2985,
Pongo abelii	ENSPPYG00000015628	1 retrocopy	retro_pabe_3452 ,