RetrogeneDB ID: retro_mmul_2289

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:53978697..53979605(+)
• Located in intron of: ENSMMUG00000028994

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSMMUG00000000442
• Aliases: BRIX1, BXDC2
• Description: ribosome biogenesis protein BRX1 homolog [Source:RefSeq peptide;Acc:NP_001248176]

Sequence

>retro_mmul_2289
GTGGCAGCAACCAAGAGGAAACAGTATGGAGGCGTGGCAATTCAGACAAAGAACCCAAAAAGAAACAAAAAAGAGGACGA
GTGGCCAGCTAAGCTGAGAGCCACCGCAGAGGAGGTGGAGGAAGAAGATGGAGACTGGATCCCAGGCCGTGTTTGCAAGG
GAGAGTGAAAAAACAAGGAATGGATTTTCATCTTTTCTCCCAGAGGAATAAATAAATTTCAGAACAAGACATTTTATGCA
GGACTTGAGAATGTTGATGCCTCATTCTAAAGCAGACACTAAAGTGGATCGTAAGTATAAATAATTTGTGATTAGCGAGC
TCTGTGAAATGAAAAACTGTAATAAATGCATATACTTTGAAGCTAAGAAAAAACAGGATCTCTTTATGTAGCTTTCAAAT
TCATCTCATGGACCATCTGCTAAATTTCTTGTTCAAAATATTCATACCCTAGCTGAACTAAAGATAACTGGAAACTGTTT
GAAAGGTTCTCGGCCCCTTTTGCCTTGACCCAGCTTTTGATGAATTACTACATTATGGTTTGTTAAAGGAACTCTTAATT
CAGATCTTTAGTACACTGTGCTATCATCCCAAAAGCCAACCATTCATGGTCCATGTGTTCACTTTCATCTTTTTGGATAA
TAGGATATGGTTTCAGAAGTTTCATATCATAGAAGAAGATGTTCCTCTTGTAGAAATAGGACCTTGTTTTGTCTTAAATC
TCATAAACATTATTCAGGGAAGTTTTGGAGGATCAACTTTATATGAAAATTCTCACCACCAGGCACCAAAAATGCATTGC
CATGTCACAATATCCATCACACCTGCAAAATACAGAGAGAGTCAGCAAGTGAAAGATGTGCAGAAACTGAGAAAGAAAGT
GCCAAAGATCGTTCTTCCTCCTGATCCC

Alignment

ORF - retro_mmul_2289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.08 %
• Parental protein coverage: 85.55 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAATKRKRRGGLAVQAKKPKRNEKDAAPPTKRHTTAEEVEEEERDRIPGPVCKGKWKNKERILIFSSRGI
          .AATKRK..GG.A.Q.K.PKRN.K....P.K...TAEEVEEE..D.IPG.VCKG..KNKE.I.IFS.RGI
Retrocopy VAATKRKQYGGVAIQTKNPKRNKKEDEWPAKLRATAEEVEEEDGDWIPGRVCKGE*KNKEWIFIFSPRGI

Parental  N-FRTR-HLMQDLRMLMPHSKADTKMDRKDKLFVINEVCEMKNCNKCIYFEAKKKQDLYMWLSNSPHGPS
          N.F....H.MQDLRMLMPHSKADTK.DRK.K.FVI.E.CEMKNCNKCIYFEAKKKQDL.M.LSNS.HGPS
Retrocopy NKFQNK>HFMQDLRMLMPHSKADTKVDRKYK*FVISELCEMKNCNKCIYFEAKKKQDLFM*LSNSSHGPS

Parental  AKFLVQNIHTLAELKMTGNCLKGSRPLLSFDPAF-DELPHYALLKELLIQIFSTPRYHPKSQPFVDHVFT
          AKFLVQNIHTLAELK.TGNCLKGSRPLL...P.F.DEL.HY.LLKELLIQIFST..YHPKSQPF..HVFT
Retrocopy AKFLVQNIHTLAELKITGNCLKGSRPLLP-*PSF>DELLHYGLLKELLIQIFSTLCYHPKSQPFMVHVFT

Parental  FTILDNRIWFRNFQIIEEDAALVEIGPRFVLNLIKIFQGSFGGPTLYENPHYQSPNMHRRVIRSITAAKY
          F..LDNRIWF..F.IIEED..LVEIGP.FVLNLI.I.QGSFGG.TLYEN.H.Q.P.MH..V..SIT.AKY
Retrocopy FIFLDNRIWFQKFHIIEEDVPLVEIGPCFVLNLINIIQGSFGGSTLYENSHHQAPKMHCHVTISITPAKY

Parental  REKQQVKDVQKLRKKEPKTLLPHDP
          RE.QQVKDVQKLRKK.PK..LP.DP
Retrocopy RESQQVKDVQKLRKKVPKIVLPPDP

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	8.29 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.55 RPM
SRP007412_cerebellum	0.00 RPM	11.43 RPM
SRP007412_heart	0.00 RPM	5.42 RPM
SRP007412_kidney	0.00 RPM	7.86 RPM
SRP007412_liver	0.00 RPM	2.30 RPM
SRP007412_testis	0.00 RPM	6.52 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2289 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001790	2 retrocopies	retro_chof_1664, retro_chof_1776,
Callithrix jacchus	ENSCJAG00000018506	1 retrocopy	retro_cjac_1389,
Homo sapiens	ENSG00000113460	1 retrocopy	retro_hsap_3954,
Gorilla gorilla	ENSGGOG00000004225	1 retrocopy	retro_ggor_2657,
Loxodonta africana	ENSLAFG00000007249	1 retrocopy	retro_lafr_1116,
Myotis lucifugus	ENSMLUG00000029255	3 retrocopies	retro_mluc_1402, retro_mluc_707, retro_mluc_963,
Macaca mulatta	ENSMMUG00000000442	1 retrocopy	retro_mmul_2289 ,
Monodelphis domestica	ENSMODG00000020386	1 retrocopy	retro_mdom_1032,
Nomascus leucogenys	ENSNLEG00000014452	1 retrocopy	retro_nleu_533,
Otolemur garnettii	ENSOGAG00000014827	2 retrocopies	retro_ogar_3116, retro_ogar_793,
Pongo abelii	ENSPPYG00000015390	2 retrocopies	retro_pabe_3258, retro_pabe_3379,
Pan troglodytes	ENSPTRG00000016784	1 retrocopy	retro_ptro_2684,
Rattus norvegicus	ENSRNOG00000018021	1 retrocopy	retro_rnor_1140,
Tupaia belangeri	ENSTBEG00000011652	9 retrocopies	retro_tbel_1963, retro_tbel_1964, retro_tbel_2981, retro_tbel_3002, retro_tbel_3082, retro_tbel_4194, retro_tbel_4229, retro_tbel_4418, retro_tbel_954,