RetrogeneDB ID: retro_ptro_1489

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:29581888..29582510(+)
• Located in intron of: ENSPTRG00000014255

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4H
• Ensembl ID: ENSPTRG00000019287
• Aliases: None
• Description: None

Sequence

>retro_ptro_1489
GGGTCCCACGGCAGTACTGGTGGCCATGGTTCCCGTAGCCAGAAGGAGTCGCTCACAGAGCCCCCCACACAGCATATGTA
GGGAATCTACCTTTTATTATGGTTCAGGGCGACATAGATGCTATCTTTAAGGATCTCAGCATAAGGAGTGTACGGGTAGT
CAGAGACAAAGACACAGATAAATTTAAAGGATTCTGCTATATAGAATTCGATGAAGTGGATTCCCTTAAGAAAGCTTGAC
ATACGATGGTGCACTGTTGGGCAATCAGTCACTTCATGTGGACACTGCAGAAGGCAGAAAACAAGATAAAGGTGGCTTTG
GATTCAGAAAAGGTGTACCAGATGACGAAGCTTCAGGGATGACTTCTTAGGAGGCAGGGGAGGTAGTCACCCAGGTGACC
GGGAAACAGGCCCCCGACTGGGCAGCCACTTCAGAGATGGTCCTCCCTTCCACCATCCAACATGGATTTCAAAGAACCGA
CAGAGGAGGGAAGAGCACAAAGACCACGACTCCAGCTTAAACCTCGTATGTTGTGACGCCCCTCAATCAAGTAGCTGATC
CCAACTCTGCTATCTTCAGGGGTGCCAGACCCAGAGTGGAATTCATTCACAAGGAGCAAGAA

Alignment

ORF - retro_ptro_1489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.24 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GSRGSAGGHGSRSQKELPTEPP-YTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVE
          GS.GS.GGHGSRSQKE..TEPP..TAYVGNLPF..VQGDIDAIFKDLSIRSVR.VRDKDTDKFKGFCY.E
Retrocopy GSHGSTGGHGSRSQKESLTEPP<HTAYVGNLPFIMVQGDIDAIFKDLSIRSVRVVRDKDTDKFKGFCYIE

Parental  FDEVDSLK-EALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDD-RGFRDDFLGGRGGSRPGDRRT
          FDEVDSLK.E.LTYDGALLG..SL.VD.AEGRKQDKGGFGFRKG.PDD.R.FRDDFLGGRGGS.PGDR.T
Retrocopy FDEVDSLK<ESLTYDGALLGNQSLHVDTAEGRKQDKGGFGFRKGVPDD<RSFRDDFLGGRGGSHPGDRET

Parental  GPPMGSRFRDGPP-LRGSNMDFREPTEEERAQRPRLQLKPRT-VATPLNQVANPNSAIFGGARPREEVVQ
          GP..GS.FRDGPP.L..SNMDF.EPTEE.RAQRPRLQLKPR..V.TPLNQVA.PNSAIF.GARPR.E...
Retrocopy GPRLGSHFRDGPP<LPPSNMDFKEPTEEGRAQRPRLQLKPRM<VVTPLNQVADPNSAIFRGARPRVEFIH

Parental  KEQE
          KEQE
Retrocopy KEQE

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	1.29 RPM	249.10 RPM
SRP007412_cerebellum	2.94 RPM	376.95 RPM
SRP007412_heart	0.20 RPM	166.25 RPM
SRP007412_kidney	0.26 RPM	237.30 RPM
SRP007412_liver	0.03 RPM	273.10 RPM
SRP007412_testis	1.26 RPM	160.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1489 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1489 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2555
Gorilla gorilla	retro_ggor_1598
Pongo abelii	retro_pabe_1879
Macaca mulatta	retro_mmul_619

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 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,
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,