RetrogeneDB ID: retro_mmul_1135

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:13537643..13538051(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2378
• Ensembl ID: ENSMMUG00000019919
• Aliases: None
• Description: proteasome subunit beta type-1 [Source:RefSeq peptide;Acc:NP_001247565]

Sequence

>retro_mmul_1135
GCTGCAGCAGTGCACTGTGGTCCTCCACAGCCACTCGGGTCCCTGACAGTGGAGCTGCTCAGCCCCGCGGGCTCCTTAGG
ACTGTACGTGTCATCCTATGTTTTCAATGGAGATACTGGTTTGGCAACAGCTGCACAAGACTTTTGCATTGCCACTTCTG
ACACTCTGTTGAGTCAAGGGTTTCAATTAACACCTGGGACAACCCCAAATGTTACAAATTAACAGACAAAACAGTCATTG
GATGCAGTGGTTTTCATGGAGACTGTCTTCCCTGACAAAGATTATTGCAGCAAAACTAAAGATGTATAAACATCCTAATA
ATAAGGCCATGACTACTGGGGCAATTGGAATGTTATTTACAATCCTGTATCCAGGCACTACTGTCCATACGATGGTTACA
ACATCGTC

Alignment

ORF - retro_mmul_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.12 %
• Parental protein coverage: 56.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVAMYSAPGRDLG---MEPHGAAGPLQLRFSPYAFNGGTVLAIAGEDFAIVASDTRLSEGF-SIHTRDSP
          ..A....P...LG....E....AG.L.L..S.Y.FNG.T.LA.A..DF.I..SDT.LS.GF.SI.T.D.P
Retrocopy AAAVHCGPPQPLGSLTVELLSPAGSLGLYVSSYVFNGDTGLATAAQDFCIATSDTLLSQGF<SINTWDNP

Parental  KCYKLTDKTVIGCSGFHGDCL-TLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILY-SRRFFPYYVYNI
          KCYKLTDKTVIGCSGFHGDCL..LTKII.A.LKMYKH.NNKAMTTGAI..ML.TILY.SR...PY..YNI
Retrocopy KCYKLTDKTVIGCSGFHGDCL<SLTKIIAAKLKMYKHPNNKAMTTGAI-GMLFTILY<SRHYCPYDGYNI

Parental  I
          .
Retrocopy V

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	47.29 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	61.80 RPM
SRP007412_cerebellum	0.00 RPM	32.93 RPM
SRP007412_heart	0.00 RPM	36.16 RPM
SRP007412_kidney	0.12 RPM	59.39 RPM
SRP007412_liver	0.08 RPM	77.07 RPM
SRP007412_testis	0.00 RPM	42.29 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1135 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1135 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135 ,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,