RetrogeneDB ID: retro_mmul_2634

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:119534154..119534897(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000016648
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2634
ATGGTGGACTTCGATACCTACGACAATCGGGCCTACAGCAGGTTTGGCAGGGCAGAGGGTCCCGCCGCAGTGCTGGTGGC
CATGGTTCCCGTAGCCAGAAGGAGTTGCCCACAGAGACCCCCTACACAGCCTACTTAGGAAATCTACCTTTTAATAAGGT
TCAGGGTGACATAGATGCTATCTTTACGGATCTCAGTATAAGGAGTGTACGGCTAGTCAGAGACAAAGACACAGATCAAT
TTAAAGGATTCTGCTATGTAGAATTCGATGAAGCAGATTCCCTTAAGGAAGCCTTGACATACAATGGTGCACTGTTGGGC
AATGGGTCACTTCATGTGGACATTGCAGAAGGCAGAAAACAAGATAAAGGTGGCTTTGGATTCAGAACAGGTGGACCAGA
TGACAGAGGAATGGGTAGCTCTGGAGAATCTAGAGGTGGATGGGATTCCCTGGATAACTTCAATTCTGGCTTCAGGGATG
ACTTCTTAGGGAGCAGGGGAGGTAGTCGCCCAGGTGACCGGGGAACAGCTCCCGCCATGGGCAGCCGCTTTAGAGATGGC
CCTCCCCTCCGCGGATCCAACATGGATTTCAGAGAACCCACAGAAGAGGAAAGAGCACAGGGACCATGACTCCAGCTTAA
ACCTCGAACAGTGGCGACACCCCTCAATCAAGTAGCCAATCCCAACTCTGCTATCTTCGGAGGTGCCAGGCCTAGAGAGG
AAGTCCTTCCAAAAGAGCAAGAA

Alignment

ORF - retro_mmul_2634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADFDTYDDRAYSSFGG-GRGSRGSAGGHGSRSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRS
          M.DFDTYD.RAYS.FG..GRGSR.SAGGHGSRSQKELPTE.PYTAY.GNLPFN.VQGDIDAIF.DLSIRS
Retrocopy MVDFDTYDNRAYSRFGR<GRGSRRSAGGHGSRSQKELPTETPYTAYLGNLPFNKVQGDIDAIFTDLSIRS

Parental  IRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRGMG
          .RLVRDKDTD.FKGFCYVEFDE.DSLKEALTY.GALLG..SL.VDIAEGRKQDKGGFGFR.GGPDDRGMG
Retrocopy VRLVRDKDTDQFKGFCYVEFDEADSLKEALTYNGALLGNGSLHVDIAEGRKQDKGGFGFRTGGPDDRGMG

Parental  SSRESRGGWDSRDDFNSGFRDDFLGGRGGSRPGDRRTGPPMGSRFRDGPPLRGSNMDFREPTEEERAQRP
          SS.ESRGGWDS.D.FNSGFRDDFLG.RGGSRPGDR.T.P.MGSRFRDGPPLRGSNMDFREPTEEERAQ.P
Retrocopy SSGESRGGWDSLDNFNSGFRDDFLGSRGGSRPGDRGTAPAMGSRFRDGPPLRGSNMDFREPTEEERAQGP

Parental  RLQLKPRTVATPLNQVANPNSAIFGGARPREEVVQKEQE
          .LQLKPRTVATPLNQVANPNSAIFGGARPREEV..KEQE
Retrocopy *LQLKPRTVATPLNQVANPNSAIFGGARPREEVLPKEQE

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	0.11 RPM	191.49 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	252.75 RPM
SRP007412_cerebellum	0.26 RPM	185.78 RPM
SRP007412_heart	0.18 RPM	122.01 RPM
SRP007412_kidney	0.12 RPM	133.10 RPM
SRP007412_liver	0.08 RPM	104.86 RPM
SRP007412_testis	0.08 RPM	121.64 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2634 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2634 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2634 has 0 orthologous retrocopies within eutheria group .

---

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,