RetrogeneDB ID: retro_mmul_2450

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:63747829..63748541(-)
• Located in intron of: ENSMMUG00000011281

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1866
• Ensembl ID: ENSMMUG00000003702
• Aliases: None
• Description: eukaryotic translation initiation factor 4A2 [Source:RefSeq peptide;Acc:NP_001182590]

Sequence

>retro_mmul_2450
AGAAGATACCTTTTTCCAAAATGGATCAAAATGTTAGTTTTGGATGAAGCAGATGAAATGTTCAGCCAAGGGTTTAATGA
TCAAATCTATGAGATTTTCCCAAAAATTAAATATAAGTATTTAGGTTGTGTTGCTTTCTGCCACGATGCCAACTGATGTG
TTGGAAGTGACCAAAAAATTCACTAAAGATCCAATTCAAATTCTGGTGAAAAAGGAAGAATTGAACCTTGAAGGAATCAA
ACAGTTTTATATCAATGTTAAGCGAGAGGAATGGAAGTTGGATACACTTTGTGATTTGTACAAAACACCATTAAACAGGC
TGTTATTTTTCTCAATACAAGGTGCAAGGTGGACTGGCTGGCTGAGAAAATTCATGCCAGGGACTTCACAGTTTTTGCTC
TGCATGGTGACGTGGACCAGAAGGAGAGAGATATTATCATGAGGGAATTCCGATCAGGGTCAAGCCCTGTTCCGATCACT
ACTGACTTGTTGGCACGTGGGACTGATGTCCAAGTGTCTTTGGTTATAAACTATGATCTACCTACCAGTCATGAAAACTA
TATTCACAGAATTGGCAGAAGGGGTCGATTTAGTAGAAAAGGTGTGGCTATAAACTTTGCTACTGAAGAAGACAAGAAGA
TTCTTCGTGACACTGAGATTTTTCTACAATACTACAGTGAAGGAAATGCCCATAAATGTAGCTGATTGTATT

Alignment

ORF - retro_mmul_2450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.4 %
• Parental protein coverage: 76.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIF-QKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILV
          RRYL.PKWIKM.VLDEADEM.S.GF.DQIYEIF.QKLN.SI.VVLLSATMPTDVLEVTKKF..DPI.ILV
Retrocopy RRYLFPKWIKMLVLDEADEMFSQGFNDQIYEIF>QKLNISI*VVLLSATMPTDVLEVTKKFTKDPIQILV

Parental  KKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIF-LNTRRKVDWLTEKMHARDFTVSALHGD
          KKEEL.LEGIKQFYINV.REEWKLDTLCDLY.T........F.LNTR.KVDWL.EK.HARDFTV.ALHGD
Retrocopy KKEELNLEGIKQFYINVKREEWKLDTLCDLYKT-PLNRLLFF<LNTRCKVDWLAEKIHARDFTVFALHGD

Parental  MDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINF
          .DQKERD.IMREFRSGSS.V.ITTDLLARG.DV.QVSLVINYDLPT..ENYIHRIGR.GRF.RKGVAINF
Retrocopy VDQKERDIIMREFRSGSSPVPITTDLLARGTDV-QVSLVINYDLPTSHENYIHRIGRRGRFSRKGVAINF

Parental  VTEEDKRILRDIET-FYNTTVEEMPMNVADLI
          .TEEDK.ILRD.E..FYNTTV.EMP.NVAD.I
Retrocopy ATEEDKKILRDTEI>FYNTTVKEMPINVADCI

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	0.00 RPM	778.64 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	563.01 RPM
SRP007412_cerebellum	0.13 RPM	774.51 RPM
SRP007412_heart	0.00 RPM	298.90 RPM
SRP007412_kidney	0.12 RPM	278.40 RPM
SRP007412_liver	0.04 RPM	112.18 RPM
SRP007412_testis	0.08 RPM	130.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2450 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2450 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_593
Pan troglodytes	retro_ptro_437
Gorilla gorilla	retro_ggor_525
Pongo abelii	retro_pabe_596

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014724	2 retrocopies	retro_btau_258, retro_btau_522,
Canis familiaris	ENSCAFG00000013659	1 retrocopy	retro_cfam_378,
Cavia porcellus	ENSCPOG00000011183	1 retrocopy	retro_cpor_639,
Dasypus novemcinctus	ENSDNOG00000011502	5 retrocopies	retro_dnov_1264, retro_dnov_2018, retro_dnov_2066, retro_dnov_648, retro_dnov_869,
Echinops telfairi	ENSETEG00000018565	3 retrocopies	retro_etel_1174, retro_etel_2164, retro_etel_451,
Homo sapiens	ENSG00000156976	2 retrocopies	retro_hsap_593, retro_hsap_878,
Gorilla gorilla	ENSGGOG00000005867	2 retrocopies	retro_ggor_525, retro_ggor_712,
Macropus eugenii	ENSMEUG00000011737	1 retrocopy	retro_meug_237,
Microcebus murinus	ENSMICG00000007377	1 retrocopy	retro_mmur_525,
Macaca mulatta	ENSMMUG00000003702	2 retrocopies	retro_mmul_1055, retro_mmul_2450 ,
Macaca mulatta	ENSMMUG00000009590	1 retrocopy	retro_mmul_851,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Nomascus leucogenys	ENSNLEG00000006633	1 retrocopy	retro_nleu_2589,
Oryctolagus cuniculus	ENSOCUG00000005011	3 retrocopies	retro_ocun_392, retro_ocun_696, retro_ocun_763,
Otolemur garnettii	ENSOGAG00000010729	2 retrocopies	retro_ogar_2830, retro_ogar_943,
Ochotona princeps	ENSOPRG00000004170	1 retrocopy	retro_opri_498,
Pongo abelii	ENSPPYG00000014384	2 retrocopies	retro_pabe_596, retro_pabe_677,
Pan troglodytes	ENSPTRG00000015718	1 retrocopy	retro_ptro_437,
Rattus norvegicus	ENSRNOG00000001815	2 retrocopies	retro_rnor_1163, retro_rnor_2340,
Ictidomys tridecemlineatus	ENSSTOG00000012601	1 retrocopy	retro_itri_858,
Tupaia belangeri	ENSTBEG00000002268	11 retrocopies	retro_tbel_114, retro_tbel_1488, retro_tbel_1500, retro_tbel_2048, retro_tbel_2524, retro_tbel_2729, retro_tbel_2733, retro_tbel_3159, retro_tbel_3793, retro_tbel_4599, retro_tbel_841,
Takifugu rubripes	ENSTRUG00000005660	2 retrocopies	retro_trub_14, retro_trub_6,
Tarsius syrichta	ENSTSYG00000013050	3 retrocopies	retro_tsyr_1905, retro_tsyr_903, retro_tsyr_935,