RetrogeneDB ID: retro_ggor_1598

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 22:15014689..15015308(+)
• Located in intron of: ENSGGOG00000003475

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4H
• Ensembl ID: ENSGGOG00000005284
• Aliases: None
• Description: None

Sequence

>retro_ggor_1598
TCCCACAGCAGTACTGGTGGCCATGGTTCCCGTAGCCAGAAGGAGTCGCTCACAGAGCACCCCCCAGAGCATATGTAGGG
AATCTACCTTTTAATATGGTTCAGGGCGACATAGATGCTATCTTTAAGGATCTCAGCATAAGGAGTGTACGGGTAGTCAG
AGACAAAGACACAGATAAATTTAAAGGATTCTGCTATATAGAATTCGATGAAGTGGATTCCCTTAAGGAAGCTTGCCATA
CGATGGTGCACTGTTGGGCAATCAGTCACTTCATGTGGACATTGCAGAAGGCAGAAAACAAGATAAAGGTGGCTTTGGAT
TCAGAAAAGGTGTACCAGATGACGAAGCTTCAGGGATGACTTCTTAGGAGGCAGGGCAGGTAGTCACCCAGGTGACTGGG
AAACAGGCCCCCGACTGGGCAGCCACTTCAGAGATGGTCCTCCCTTCCACGATCCAACATGGATTTCAAAGAACCGACAG
AGGAGGGAAGAACACAAAGACCACGACTCCAGCTTAAACCTCAAATGTTGTGACGCCCCTCAATCAAGTAGCCGATCCCA
ACTCTGCTATCTTCAGGGGTGCCAGACCCAGAGTGGAATTCGTTCACAAGGAGCAAGAA

Alignment

ORF - retro_ggor_1598 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.28 %
• Parental protein coverage: 90.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SRGSAGGHGSRSQKELPTE-PPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEF
          S..S.GGHGSRSQKE..TE..P..AYVGNLPFN.VQGDIDAIFKDLSIRSVR.VRDKDTDKFKGFCY.EF
Retrocopy SHSSTGGHGSRSQKESLTE<APPRAYVGNLPFNMVQGDIDAIFKDLSIRSVRVVRDKDTDKFKGFCYIEF

Parental  DEVDSLKEA-LTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDD-RGFRDDFLGGRGGSRPGDRRTG
          DEVDSLKEA.L.YDGALLG..SL.VDIAEGRKQDKGGFGFRKG.PDD.R.FRDDFLGGR.GS.PGD..TG
Retrocopy DEVDSLKEA<LPYDGALLGNQSLHVDIAEGRKQDKGGFGFRKGVPDD<RSFRDDFLGGRAGSHPGDWETG

Parental  PPMGSRFRDGPP-LRGSNMDFREPTEEERAQRPRLQLKPR-TVATPLNQVANPNSAIFGGARPREEVVQK
          P..GS.FRDGPP.L..SNMDF.EPTEE.R.QRPRLQLKP...V.TPLNQVA.PNSAIF.GARPR.E.V.K
Retrocopy PRLGSHFRDGPP<LPRSNMDFKEPTEEGRTQRPRLQLKPQ<NVVTPLNQVADPNSAIFRGARPRVEFVHK

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	2.40 RPM	303.36 RPM
SRP007412_cerebellum	2.92 RPM	291.11 RPM
SRP007412_heart	0.38 RPM	102.22 RPM
SRP007412_kidney	0.41 RPM	170.42 RPM
SRP007412_liver	0.24 RPM	141.04 RPM
SRP007412_testis	0.93 RPM	153.53 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1598 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2555
Pan troglodytes	retro_ptro_1489
Pongo abelii	retro_pabe_1879
Macaca mulatta	retro_mmul_619

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 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 ,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
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,
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,