RetrogeneDB ID: retro_pabe_1559

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:48388103..48388880(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR45L
• Ensembl ID: ENSPPYG00000008785
• Aliases: WDR45B, WDR45L, WIPI3
• Description: WD repeat domain phosphoinositide-interacting protein 3 [Source:RefSeq peptide;Acc:NP_001127514]

Sequence

>retro_pabe_1559
ATGATCCTCCTACCCTGTAACTCCCACAGTAACTAGCTGCTCGACACCGGCTTCAGCCAGGACCACGGATGCCTTGCTTG
TGGGATGGAAAACGGATTCTGAGTCTATAACACCAATCCATTAAAAGAAAAAGAGAAACAAAAATTTCTAGGTGGAAGAA
TTGGCCATAATGAAATGTTATTTTGCTGCAACTATTTAGCTTTAGTTGTTGGTGGAAAAAAGCCAAAATGCCTTCCCAAC
AAAGTGATGATCTGAGATGACTGAAAAAGACGACTGTTAATGAAATAGAATTTGCTACAGAAGTCAAGGCAGTCAAATTG
CAGCGAGATAGAATTGTGGTTGTTTTGGACTCCATGATTAAGGTGTTTGCACTCACACAGAACCCCCATCAGTTGTACAT
CTTTGAAACCTCCTAAAACCCTAAAGGCCTCTGTCCTCTGTTCCAGTAGCAACAACTCTCTTCTGGCCTTGCTAGGCACG
CACATGGGCCATGTTCAGCTCGTGGACTGGGCCAGCACAGAGAAGCCACCTGTGGACATTCCCGCTCCTGAGGGCATCCT
GAGCTGCATCACACTCAACCTCCAGGGAACAAGAATTGCAACCACACTCACAAAAGGGACCCTTATAAGAATAGTTGATA
CTTCATCAGGACATTTAATCCAGGAACTATGAAGAGGATCTCAAGTAGCTAATGTTTTCTGCATTAACTTCAATCAAGAT
GCGTCCTTCATCTGCATATCCAGTGACCACAGCACAGTGCACATTTTTGCAGCTGAA

Alignment

ORF - retro_pabe_1559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.48 %
• Parental protein coverage: 75.58 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNLLPCNPHGNGLLYAGFNQDHGCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCNYLALVG
          M.LLPCN.H.N.LL..GF.QDHGC.ACGMENGF.VYNT.PLKEKEKQ.FL.G..GH.EMLF.CNYLALV.
Retrocopy MILLPCNSHSN*LLDTGFSQDHGCLACGMENGF*VYNTNPLKEKEKQKFLGGRIGHNEMLFCCNYLALVV

Parental  GGKKPKYPPNKVMIWDD-LKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPHQLHVFETCY
          GGKKPK..PNKVMI.DD.LKK.TV.EIEF.TEVKAVKL.RDRIVVVLDSMIKVF..T.NPHQL..FET..
Retrocopy GGKKPKCLPNKVMI*DD<LKKTTVNEIEFATEVKAVKLQRDRIVVVLDSMIKVFALTQNPHQLYIFETS*

Parental  NPKGLCVL-CPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCIALNLQGTRIATASEKGT
          NPKGLC.L.....N..L.A..GTH.GHVQLVD.ASTEKPPVDIPA.EG.LSCI.LNLQGTRIAT...KGT
Retrocopy NPKGLCPL>SSSNNSLL-ALLGTHMGHVQLVDWASTEKPPVDIPAPEGILSCITLNLQGTRIATTLTKGT

Parental  LIRIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAE
          LIRI.DTSSGHLIQEL.RGSQ.AN..CINFNQDAS.IC.SSDH.TVHIFAAE
Retrocopy LIRIVDTSSGHLIQEL*RGSQVANVFCINFNQDASFICISSDHSTVHIFAAE

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	0.06 RPM	45.78 RPM
SRP007412_cerebellum	0.00 RPM	40.49 RPM
SRP007412_heart	0.00 RPM	12.01 RPM
SRP007412_kidney	0.07 RPM	35.20 RPM
SRP007412_liver	0.12 RPM	14.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1559 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1559 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1879
Gorilla gorilla	retro_ggor_1376
Macaca mulatta	retro_mmul_1330

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005657	1 retrocopy	retro_cpor_322,
Homo sapiens	ENSG00000141580	2 retrocopies	retro_hsap_1820, retro_hsap_1879,
Gorilla gorilla	ENSGGOG00000006132	2 retrocopies	retro_ggor_1376, retro_ggor_2173,
Macropus eugenii	ENSMEUG00000013344	1 retrocopy	retro_meug_233,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330,
Mus musculus	ENSMUSG00000025173	1 retrocopy	retro_mmus_1487,
Nomascus leucogenys	ENSNLEG00000010516	1 retrocopy	retro_nleu_1227,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559 ,
Pongo abelii	ENSPPYG00000020333	1 retrocopy	retro_pabe_2481,
Pan troglodytes	ENSPTRG00000009807	3 retrocopies	retro_ptro_1171, retro_ptro_1262, retro_ptro_2912,
Pteropus vampyrus	ENSPVAG00000006212	1 retrocopy	retro_pvam_158,