RetrogeneDB ID: retro_pabe_1879

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:25865866..25866493(+)
• Located in intron of: ENSPPYG00000011720

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_1879
AGAGGGTCCCACGGCAGTACTGGTGGCTATGGTTCCCGTAGCCAGAAGGGGTCGCTCAGAGAGCCCCCCACACAGCATAC
GTAGGAAATCAACCTTTTAATATGGTTCAGGGTGACATAGATGCTATCTTTAAGGATCTCAGCATCAAGAGTGTACGGGT
AGTCAGAGACAAAGATACAGATAAATTTAAAGGATTCTGCTGTATACAATTCGATGAAGTGGATTCCCTTAAGGAAGCTT
GACATACAATGGTGTACCGTTGGGCAATCAGTCACTTAATGTGGACATTGCAGAAGGCAGAAAACAAGATAAAGGTGGCT
TTGGATTCAGAAAAGGTGTACCAGATGACGAGGCTTCAGGGATGACTTCTTAGGAGGCAGGAGAGGTAGTCACCCAGGTG
ACTGGCAAACAGGCCCCCCAGTGGGCAGCCACTTCAGAGATGGTCCTCCCCTCCACCAATACAACATGGATTTCAAAGAA
CCGAGAGAGGAGGGAAGAGCACAAAGACCATGACTCCAGCTTAAACCTCGAACGGTTGTGACGCCCCTCAATCAAGTAGC
CAATCCCAACTCTGCTATCTTCAGGAGTGCCAGACCCAGAGTGGAATTCATTCACAAGGAGCAAGAA

Alignment

ORF - retro_pabe_1879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.4 %
• Parental protein coverage: 92.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RGSRGSAGGHGSRSQKELPTEPP-YTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYV
          RGS.GS.GG.GSRSQK....EPP..TAYVGN.PFN.VQGDIDAIFKDLSI.SVR.VRDKDTDKFKGFC..
Retrocopy RGSHGSTGGYGSRSQKGSLREPP<HTAYVGNQPFNMVQGDIDAIFKDLSIKSVRVVRDKDTDKFKGFCCI

Parental  EFDEVDSLKEA-LTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDD-RGFRDDFLGGRGGSRPGDRR
          .FDEVDSLKEA.LTY.G..LG..SL.VDIAEGRKQDKGGFGFRKG.PDD.RGFRDDFLGGR.GS.PGD..
Retrocopy QFDEVDSLKEA<LTYNGVPLGNQSLNVDIAEGRKQDKGGFGFRKGVPDD<RGFRDDFLGGRRGSHPGDWQ

Parental  TGPAMGSRFRDGPPLRGSNMDFREPTEEERAQRPRLQLKPRTVATPLNQVANPNSAIFGGARPREEVVQK
          TGP..GS.FRDGPPL...NMDF.EP.EE.RAQRP.LQLKPRTV.TPLNQVANPNSAIF..ARPR.E...K
Retrocopy TGPPVGSHFRDGPPLHQYNMDFKEPREEGRAQRP*LQLKPRTVVTPLNQVANPNSAIFRSARPRVEFIHK

Parental  EQE
          EQE
Retrocopy EQE

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	3.32 RPM	65.91 RPM
SRP007412_cerebellum	7.66 RPM	42.44 RPM
SRP007412_heart	0.21 RPM	23.15 RPM
SRP007412_kidney	0.23 RPM	34.41 RPM
SRP007412_liver	0.03 RPM	21.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1879 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1879 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1879 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2555
Pan troglodytes	retro_ptro_1489
Gorilla gorilla	retro_ggor_1598
Macaca mulatta	retro_mmul_619

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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,