RetrogeneDB ID: retro_mmul_1558

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:45464088..45464893(+)
• Located in intron of: ENSMMUG00000004717

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1427
• Ensembl ID: ENSMMUG00000006007
• Aliases: None
• Description: proteasome subunit beta type-5 [Source:RefSeq peptide;Acc:NP_001247774]

Sequence

>retro_mmul_1558
ACACTAGACATGGTGCTGGTCAGCTTGTTGGAGAGGCTGCTACTTGTGAACCAGTGCAGGTTTTCTGGACTCAAAGTTTA
TGCAGATCTGCTGGATCTGGGTCCAGGGAGTCCCAGTGATGGGCTGATCCTGGCCATGCCCAGCTGGGGAGTCTCAGATG
AGCAGGGAATCAAAATGCTTCATGGAATCACCACCCTGGTCTTCAAGTTCTGGCATGGAGTCATAGTTGCAGCAGACTAT
AGGACCACAGTGGGTGCTTACATTGCCTCCAGATGGTAAAAAAGGTGGCACAGATCAACCCCTACCTGAAGCCATCATGG
CTAGGGGCACAGCAAATTGTAGCTTCTGAGAATGGCTGTTGGCTCAGCAATGTCAAATGTATGAGCTTTGAAATAAGGAA
TGCATCTCTGTAGCAGCTGCCTTCCAGCTGCTTGCCAACATATTGCACCAGTACAAAGGCAGGGGGCTATCCATGGGCAA
CATGATCTGTGGCTGGGATAGGAGAGGCCCTGGCCTCTGCTACACGGACACTGAAGGGAATCAGATCTCGGGGGCCACCT
TCTCTGTAGGTTCTGGCTCTGTGTATGCTTATGGGGTTATGAATCAGGGCTATTCCTATAACCTGGAAATGGAGCCGGTC
TATGATCTGGCCCATGAAGCGAGCTACCAAGCCATCTATTAAGCCACCTGCATAGATGCCTACTCAGGAGGTGCTGCTAA
CCTCTACCACGTGCAGGAGGATGGCTGGATCCAAGTCTCCAGTGACAATGCAGTTGGTCTTCATAAGTATGACGGATCTA
CCCCA

Alignment

ORF - retro_mmul_1558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TLDMALASVLERPLPVNQRGFFGLGGRADLLDIGPGSPSDGLSLAAPGWGVPEEPGIEMLHGTTTLAFKF
          TLDM.L.S.LER.L.VNQ..F.GL...ADLLD.GPGSPSDGL.LA.P.WGV..E.GI.MLHG.TTL.FKF
Retrocopy TLDMVLVSLLERLLLVNQCRFSGLKVYADLLDLGPGSPSDGLILAMPSWGVSDEQGIKMLHGITTLVFKF

Parental  RHGVIVAADSRATAGAYIAS-QTVKKVIEINPYLLGT-MAGGAADCSFWERLLARQCRIYELRNKERISV
          .HGVIVAAD.R.T.GAYIAS.Q.VKKV..INPYL....MA.G.A.CSF.E.LLA.QC..YEL.NKE.ISV
Retrocopy WHGVIVAADYRTTVGAYIAS<QMVKKVAQINPYLKPS<MARGTANCSF*EWLLAQQCQMYEL*NKECISV

Parental  AAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYD
          AAA..LLAN...QYKG.GLSMG.MICGWD.RGPGL.Y.D.EGN.ISGATFSVGSGSVYAYGVM..GYSY.
Retrocopy AAAFQLLANILHQYKGRGLSMGNMICGWDRRGPGLCYTDTEGNQISGATFSVGSGSVYAYGVMNQGYSYN

Parental  LEVEQAYDLARRAIYQ----ATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHEKYSGSTP
          LE.E..YDLA..A.YQ....AT..DAYSGGA.NLYHV.EDGWI.VSSDN...LH.KY.GSTP
Retrocopy LEMEPVYDLAHEASYQAIY*ATCIDAYSGGAANLYHVQEDGWIQVSSDNAVGLH-KYDGSTP

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	22.86 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	57.20 RPM
SRP007412_cerebellum	0.00 RPM	18.79 RPM
SRP007412_heart	0.00 RPM	26.09 RPM
SRP007412_kidney	0.00 RPM	40.61 RPM
SRP007412_liver	0.00 RPM	54.43 RPM
SRP007412_testis	0.04 RPM	31.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1558 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634, retro_hsap_95,
Gorilla gorilla	ENSGGOG00000026856	2 retrocopies	retro_ggor_1232, retro_ggor_156,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558 ,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,