RetrogeneDB ID: retro_mmul_1325

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:3748201..3748783(+)
• Located in intron of: ENSMMUG00000011466

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17236
• Ensembl ID: ENSMMUG00000014909
• Aliases: None
• Description: charged multivesicular body protein 1a [Source:RefSeq peptide;Acc:NP_001078827]

Sequence

>retro_mmul_1325
ATGGAGAAACACCTGTTCAACCTGAAGTTCGCGGCCAAAGAACTGAGCAGGAGTGCCAAAAAATGCGATAAGGAGGAAAA
GGCCGAAAAGGCCAAAATCAAAAAGGCCATTCAGAAGGGCAACATGGAAGTTGCGAGGATCCACGCCGAAAATGCCATCC
GCCAGAAGAACCAGGCGGTGAATTTCTTAAGAATGAGTGCGCGAGTCGATGCAGTGGCTGCCAGGGTCCAGACGGCGGTG
ACGATGGGCAAGGTGACCAAGTCGATGGCTGGTGTGGTTAAGTCAATGGATGCGACACTGAAGACCATGAATCTGGAGAA
GATTTCTGCCTTGATGGACAAATTCGAGCACCAGTTTGAAACTCTGGACGTCCAGACGCAGCAAATGGAGGACACGATGA
GCAGCACGACGACGCTCACCACTCCCCAGAACCAAGTGGATATGCTGCTCCAGGAAATGGCAGACGAGGCGGGCCTCGAC
CTCAACATGGAGCTGCCGCAGGGGCAGACCGGCTCCGTGGGCACGAGCGTGGCTTCGGCGGAGCAGGATGAACTGTCTCA
GAGACTGGCCCGCCTTCGGGAT

Alignment

ORF - retro_mmul_1325 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDDTLFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALQQKNVECARVYAENAIRKKNEGVNWLRMASRVD
          M...LF.LKF.AK.L...AKK..K..KAE.AK.KKA.Q..N.E.AR..AENAIR.KN..VN.LRM..RVD
Retrocopy MEKHLFNLKFAAKELSRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARVD

Parental  AVASKVQTAVTMKGVTKNMAQVTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLT
          AVA..VQTAVTM..VTK.MA.V.K..D..L.TM.L.K.S..MD.FE.Q...LDV.T..MED.MSS.TTLT
Retrocopy AVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQQMEDTMSSTTTLT

Parental  TPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
          TPQ.QVD.L....A.E.GL.....L.Q...G...VG.S......D.LS.RLA.LR.
Retrocopy TPQNQVDMLLQEMADEAGLDLNMELPQGQTG--SVGTSVASAEQDELSQRLARLRD

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	16.14 RPM	4.93 RPM
SRP007412_brain_prefrontal_cortex	23.48 RPM	26.50 RPM
SRP007412_cerebellum	8.59 RPM	4.84 RPM
SRP007412_heart	10.89 RPM	5.71 RPM
SRP007412_kidney	19.72 RPM	11.27 RPM
SRP007412_liver	8.99 RPM	24.03 RPM
SRP007412_testis	14.89 RPM	14.40 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1325 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001216	1 retrocopy	retro_amel_1749,
Bos taurus	ENSBTAG00000033331	1 retrocopy	retro_btau_1048,
Canis familiaris	ENSCAFG00000019822	1 retrocopy	retro_cfam_1866,
Callithrix jacchus	ENSCJAG00000010826	1 retrocopy	retro_cjac_1147,
Homo sapiens	ENSG00000131165	2 retrocopies	retro_hsap_359, retro_hsap_75,
Macaca mulatta	ENSMMUG00000014909	3 retrocopies	retro_mmul_1325 , retro_mmul_476, retro_mmul_706,
Mustela putorius furo	ENSMPUG00000007281	1 retrocopy	retro_mputfur_383,
Mus musculus	ENSMUSG00000000743	1 retrocopy	retro_mmus_2260,
Oryctolagus cuniculus	ENSOCUG00000023371	1 retrocopy	retro_ocun_1508,
Otolemur garnettii	ENSOGAG00000004883	1 retrocopy	retro_ogar_170,
Pongo abelii	ENSPPYG00000007667	1 retrocopy	retro_pabe_344,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311,