RetrogeneDB ID: retro_pabe_1888

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:37409260..37409703(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNPH1
• Ensembl ID: ENSPPYG00000016635
• Aliases: None
• Description: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [Source:HGNC Symbol;Acc:21218]

Sequence

>retro_pabe_1888
TTCTATGGGGTCATCCACTGAGGACAGGAGGACCGGGCCCTGTACAGGTGGATCGTGTGGCGGCTGCCATGCTTGGAGCC
AGTGCTCACCGAGCACTTGGCAGCTGTGGAGCTGGACGCGGGGTTGATAAGTCCGCTGGGGGTGACAGGCTCATCCATGA
GTGGTACTTGACGTGGCTGCAGAAGGCAGATGTGGTCGTGGCAGGAGTGACACAACTGTCCCTGGGTATAGGCTATGAAC
TGGGCCAGGCCACAGCCCTCAATAAGTGAATCCTGTGCCTGCTCCAGCCGCAGTCTGGCAGAGTGCTGTCGGCCATGATC
TGGGGAGCAGCAGATGGTTCTGGGTTCCAGGTGTGGGACTACGGAGAGGGACAGGTGGAGGCCCTGCTGCATGGATAGGT
TGAGGCTGATCCTCCCGAGCAGGTTGCCTCCCCTAACCCAACC

Alignment

ORF - retro_pabe_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.33 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FCGSIRGGRQDRTLYERIVSRLRRFGTVLTEHVAAAEM-GARGEEAAGGDRLIHEQDLEWLQQADVVVAE
          F.G.I..G..DR.LY..IV.RL.....VLTEH.AA.E..G......AGGDRLIHE..L.WLQ.ADVVVA.
Retrocopy FYGVIH*GQEDRALYRWIVWRLPCLEPVLTEHLAAVEL<GRGVDKSAGGDRLIHEWYLTWLQKADVVVAG

Parental  VTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPP
          VTQ.SLG.GYELG.A.A.NK.ILCL..PQSGRVLSAMI.GAADGS.FQVWDY.EG.VEALL....EADPP
Retrocopy VTQLSLGIGYELGQATALNK*ILCLLQPQSGRVLSAMIWGAADGSGFQVWDYGEGQVEALLHG*VEADPP

Parental  GQVAASPDPT
          .QV.ASP.PT
Retrocopy EQV-ASPNPT

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	0.77 RPM	17.20 RPM
SRP007412_cerebellum	0.97 RPM	6.57 RPM
SRP007412_heart	0.09 RPM	3.04 RPM
SRP007412_kidney	0.33 RPM	74.22 RPM
SRP007412_liver	3.03 RPM	33.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1888 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1888 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888 ,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,