RetrogeneDB ID: retro_pabe_1988

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:29375831..29376283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4H
• Ensembl ID: ENSPPYG00000017489
• Aliases: None
• Description: eukaryotic translation initiation factor 4H [Source:RefSeq peptide;Acc:NP_001125449]

Sequence

>retro_pabe_1988
ACACATAAATTTAAAGGATTCTGCTATGTAGAATTCGATGAAGTGGATTCCCATAAGGAAGCCTTGACATACGATGGTGC
ACTGTTGGGCGATCGGTCACTTCATGTGGACATTGCAGAAGACAGAAAACAAGATAAAGGTGGCTTTGGATTCAGAAAAG
GTGGACCAGATGACAGAGGCTTCAGGGTTGACTTCTTGGGGGGCAGGGGAGGTAGTCGCCCAGGTGACCGGTGAACAGGC
CCCCCCATGGGCAGCCGCTTCAGAGATGGCCCGCCCCTCCACGGATCCAACATGGATTTCAGAGAACCTACAGAAGAGGA
AAGAGCACAGAGACCACGACTCCAGCTTAAACCTCGAACAGTCGCGACGCCCCTCAATCAAGTAGCCAATCCCAACTCTG
CTATCTTCGGGGTGCCAGGCCTAGAGAGGAAGTCGTTCAAAAGGAGCAAGAA

Alignment

ORF - retro_pabe_1988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.08 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRGFRDDFLGGRG
          T.KFKGFCYVEFDEVDS.KEALTYDGALLGDRSL.VDIAE.RKQDKGGFGFRKGGPDDRGFR.DFLGGRG
Retrocopy THKFKGFCYVEFDEVDSHKEALTYDGALLGDRSLHVDIAEDRKQDKGGFGFRKGGPDDRGFRVDFLGGRG

Parental  GSRPGDRRTGPAMGSRFRDGPPLRGSNMDFREPTEEERAQRPRLQLKPRTVATPLNQVANPNSAIFG-GA
          GSRPGDR.TGP.MGSRFRDGPPL.GSNMDFREPTEEERAQRPRLQLKPRTVATPLNQVANPNSAIFG.GA
Retrocopy GSRPGDR*TGPPMGSRFRDGPPLHGSNMDFREPTEEERAQRPRLQLKPRTVATPLNQVANPNSAIFG<GA

Parental  RPREEVVQKEQE
          RPREEVVQKEQE
Retrocopy RPREEVVQKEQE

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	1.16 RPM	65.91 RPM
SRP007412_cerebellum	1.58 RPM	42.44 RPM
SRP007412_heart	0.57 RPM	23.15 RPM
SRP007412_kidney	0.73 RPM	34.41 RPM
SRP007412_liver	0.52 RPM	21.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1988 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1988 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002525	2 retrocopies	retro_chof_1279, retro_chof_1903,
Felis catus	ENSFCAG00000029386	1 retrocopy	retro_fcat_580,
Gorilla gorilla	ENSGGOG00000005284	1 retrocopy	retro_ggor_1598,
Macaca mulatta	ENSMMUG00000006205	2 retrocopies	retro_mmul_2634, retro_mmul_619,
Mus musculus	ENSMUSG00000040731	1 retrocopy	retro_mmus_3659,
Oryctolagus cuniculus	ENSOCUG00000017685	1 retrocopy	retro_ocun_1475,
Otolemur garnettii	ENSOGAG00000028051	1 retrocopy	retro_ogar_2796,
Pongo abelii	ENSPPYG00000017489	2 retrocopies	retro_pabe_1879, retro_pabe_1988 ,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Pan troglodytes	ENSPTRG00000019287	1 retrocopy	retro_ptro_1489,
Rattus norvegicus	ENSRNOG00000001454	1 retrocopy	retro_rnor_2924,
Tupaia belangeri	ENSTBEG00000009558	2 retrocopies	retro_tbel_1636, retro_tbel_2470,