RetrogeneDB ID: retro_pabe_421

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:99171281..99171472(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSPPYG00000016791
• Aliases: None
• Description: high mobility group nucleosome-binding domain-containing protein 3 [Source:RefSeq peptide;Acc:NP_001125217]

Sequence

>retro_pabe_421
ATGCAGAATAGAAAGTCTCCAGAGAATATAGAGGCAAAGATGGCTCCAAAGTAACTAAACAGGAGCCCACAAGATGGTCT
CCCAGATTGTCAGCAAAACCTCCTCCACCAAAACCTGGACCCAAACCAAGAAGAACATTTGCTAAGAAAGAACCTGGAGC
AAAGGTTAGCAGAGGTGCTAAAGAGAAGAAA

Alignment

ORF - retro_pabe_421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKSPENTE-DKDGSKVTKQEPTRRSARLSAKPAPPKPEPKPRKTSAKKEPGAKISRGAKGKK
          M..RKSPEN.E..KDGSKVTKQEPTR.S.RLSAKP.PPKP.PKPR.T.AKKEPGAK.SRGAK.KK
Retrocopy MQNRKSPENIE<GKDGSKVTKQEPTRWSPRLSAKPPPPKPGPKPRRTFAKKEPGAKVSRGAKEKK

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	25.65 RPM
SRP007412_cerebellum	0.00 RPM	63.23 RPM
SRP007412_heart	0.00 RPM	69.78 RPM
SRP007412_kidney	0.00 RPM	50.81 RPM
SRP007412_liver	0.00 RPM	25.71 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_421 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_421 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_421 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_231
Pan troglodytes	retro_ptro_200
Macaca mulatta	retro_mmul_414

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011031	1 retrocopy	retro_amel_1920,
Bos taurus	ENSBTAG00000001422	2 retrocopies	retro_btau_1524, retro_btau_1558,
Canis familiaris	ENSCAFG00000002809	1 retrocopy	retro_cfam_1013,
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Callithrix jacchus	ENSCJAG00000010800	2 retrocopies	retro_cjac_1626, retro_cjac_819,
Mustela putorius furo	ENSMPUG00000018092	1 retrocopy	retro_mputfur_1164,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Pongo abelii	ENSPPYG00000016791	1 retrocopy	retro_pabe_421 ,