RetrogeneDB ID: retro_mmul_619

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:74779004..74779617(+)
• Located in intron of: ENSMMUG00000018299

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2847
• Ensembl ID: ENSMMUG00000006205
• Aliases: None
• Description: eukaryotic translation initiation factor 4H [Source:RefSeq peptide;Acc:NP_001252991]

Sequence

>retro_mmul_619
AGTACTGGTGGCCATGGTTCCCGTAGCCAGAAGGAGTTGCCCACAGAGCCCCCCATACAATATACATAGGAAATCTACCT
TTTAATATGGTTCAGGGTGATATAGATGCTATCTTTAAGGATCTAAGCATAAGGAGTATACGGGTAGTCAGAGACAAAGA
CACAGATAAATTTAAAGGATTCTGCTATATAGAATTCAATGAAGTGGATTCCCTTAAGGAAGCTTTGACATACGATGGTA
CACTGTTGGGTAATCGGTCACTTCATGTGGACACTGCAGAAGGCAGAAAACAAGATAAAGGTGGCTCTGGATTCAGAAAA
GGTGGCCCAGATGACGAGGATTCAGGGATGACTTCTTAGGAGGCAGGGGAGGTAGTCACCCAGATGACTGGCCAACAGGC
CCCGCAATGGGCACCCATGTCAGAGATGGTCCTCCCCTCCACGGATCCAACATGGATTTCAAAGAACCAACAGAGGAGGG
AAGAGCACAAAGAACATGACTCCAGCTTAAACCTTGAACGGTTGTGATACCCCTCAATCAAGTAGCCAATCCCAACTCTG
CTATCTTCGGGGGTGCCAAACCCAGAGTGGAATTCATCCACAAAGAGCAAGAA

Alignment

ORF - retro_mmul_619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 89.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAGGHGSRSQKELPTEPP-YTAYVGNLPFNTVQGDIDAIFKDLSIRSIRLVRDKDTDKFKGFCYVEFDEV
          S.GGHGSRSQKELPTEPP..T.Y.GNLPFN.VQGDIDAIFKDLSIRSIR.VRDKDTDKFKGFCY.EF.EV
Retrocopy STGGHGSRSQKELPTEPP<HTIYIGNLPFNMVQGDIDAIFKDLSIRSIRVVRDKDTDKFKGFCYIEFNEV

Parental  DSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDD-RGFRDDFLGGRGGSRPGDRRTGPPMG
          DSLKEALTYDG.LLG.RSL.VD.AEGRKQDKGG.GFRKGGPDD.RGFRDDFLGGRGGS.P.D..TGP.MG
Retrocopy DSLKEALTYDGTLLGNRSLHVDTAEGRKQDKGGSGFRKGGPDD<RGFRDDFLGGRGGSHPDDWPTGPAMG

Parental  SRFRDGPPLRGSNMDFREPTEEERAQRPRLQLKPRTVATPLNQVANPNSAIFGGARPREEVVQKEQE
          ...RDGPPL.GSNMDF.EPTEE.RAQR..LQLKP.TV..PLNQVANPNSAIFGGA.PR.E...KEQE
Retrocopy THVRDGPPLHGSNMDFKEPTEEGRAQRT*LQLKP*TVVIPLNQVANPNSAIFGGAKPRVEFIHKEQE

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	1.57 RPM	191.49 RPM
SRP007412_brain_prefrontal_cortex	2.30 RPM	252.75 RPM
SRP007412_cerebellum	2.20 RPM	185.78 RPM
SRP007412_heart	0.06 RPM	122.01 RPM
SRP007412_kidney	0.12 RPM	133.10 RPM
SRP007412_liver	0.04 RPM	104.86 RPM
SRP007412_testis	0.41 RPM	121.64 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_619 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_619 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_619 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
Pongo abelii	retro_pabe_1879

---

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,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
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,