RetrogeneDB ID: retro_pabe_918

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:43476993..43477764(-)
• Located in intron of: ENSPPYG00000004429

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF75D
• Ensembl ID: ENSPPYG00000020747
• Aliases: None
• Description: zinc finger protein 75D [Source:HGNC Symbol;Acc:13145]

Sequence

>retro_pabe_918
ATGAGAGAGCTGAAGGCAGATGCATACTTGAACCCCCAGATGGGGGCTATGTGGGAGACTAATGGGTCTGTGAGAGAGAA
CTCCAGTCCCAGTAAGAAATGCACCACAAAAATAGGGTATCTCGGCCAGAGGGCGCTCACAGGCACTTCCAGACCTTCTG
ATACGATGAAGCAACTGGAACGCCGGAGGCTATCAGCTTACTTCAGAAATTATGCCATCAGTGATTGAGGCCAGAGATCC
ACCCAAAAGAGTAGATCTTGGAAATATTGATGTTAGAGCAGTTCCTGACCATTTTGCACAAGGATACCCAGAACTGGGTG
CAGAAGCATCACCCACAGAATGTCAAAACAGGCTCTGGTCCTGGTGAAACGCTTGCAGAGAGAACCTGGTCAAACAAAGA
ATGAGGTCACAGCCCATGAGCTGGGAGAGAAGGCAGTGCTCCTGGGAGGAACAGCAGTGGCCCCAGACTTCAAGTATAAA
CCAGCGGAGCCCCAACCAAAGGGTGTGTCTCAGAAAGAATGTTGGAATATATACTGGGTGCTACAATAGCAGCTAGGCTG
GAATACTCACAAAGAAACCCAGCCTGTGTATGAAAGAGTTGTGCATGCTCAACAGGTTTTAGCCCGTGCTGAGCAGAAAA
GCACCAAAGACTGGAAGATGGCATCTCAGCTTATCCTGCCTGAGTCCCAGAGTTTGTTGACATTTGAATAAGTGGCTGTG
TATTTTTCTGAGGAAGAATGTCAATTATTGCATCCTCCTGAGAAGACTTTA

Alignment

ORF - retro_pabe_918 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.83 %
• Parental protein coverage: 50.39 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRELNADSCSSPQMGAMWETSGSVKENSSQSKKYSTKIENLG-PESACRHFWSFRYHEATGPLETISQLQ
          MREL.AD....PQMGAMWET.GSV.ENSS.SKK..TKI..LG.PE.A.RHF..F.Y.EATG..E.IS.LQ
Retrocopy MRELKADAYLNPQMGAMWETNGSVRENSSPSKKCTTKIGYLG<PEGAHRHFQTF*YDEATGTPEAISLLQ

Parental  KLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVK-QALVLVEFLQREPDGTKNEVTA
          KLCHQ.LRPEIH.KE.ILE.L.LEQFL.IL.K.TQNWVQKHHPQNVK.QALVLV..LQREP..TKNEVTA
Retrocopy KLCHQ*LRPEIHPKE*ILEILMLEQFLTILHKDTQNWVQKHHPQNVK>QALVLVKRLQREPGQTKNEVTA

Parental  HELGKEAVLLGGTAVAPGFKWKPAEPQPMGVFQKEYWNTYRVLQEQLGWNTHKETQPVYERAVHDQQMLA
          HELG..AVLLGGTAVAP.FK.KPAEPQP.GV.QKE.WN.Y.VLQ.QLGWNTHKETQPVYER.VH.QQ.LA
Retrocopy HELGEKAVLLGGTAVAPDFKYKPAEPQPKGVSQKECWNIYWVLQ*QLGWNTHKETQPVYERVVHAQQVLA

Parental  LSELKRTKHWKMASKLILPESLSLLTFEDVAVYFSEEEWQLLNPLEKTL
          ..E.K.TK.WKMAS.LILPES.SLLTFE.VAVYFSEEE.QLL.P.EKTL
Retrocopy RAEQKSTKDWKMASQLILPESQSLLTFE*VAVYFSEEECQLLHPPEKTL

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	3.98 RPM
SRP007412_cerebellum	0.00 RPM	8.63 RPM
SRP007412_heart	0.00 RPM	2.32 RPM
SRP007412_kidney	0.00 RPM	12.23 RPM
SRP007412_liver	0.00 RPM	4.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_918 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_918 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_918 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1108
Callithrix jacchus	retro_cjac_3200

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014531	2 retrocopies	retro_cjac_3200, retro_cjac_917,
Homo sapiens	ENSG00000186376	1 retrocopy	retro_hsap_797,
Otolemur garnettii	ENSOGAG00000032383	1 retrocopy	retro_ogar_1516,
Pongo abelii	ENSPPYG00000020747	1 retrocopy	retro_pabe_918 ,