RetrogeneDB ID: retro_mmul_372

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:54198240..54198911(+)
• Located in intron of: ENSMMUG00000012055

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2373
• Ensembl ID: ENSMMUG00000011125
• Aliases: None
• Description: 26S proteasome non-ATPase regulatory subunit 7 [Source:RefSeq peptide;Acc:NP_001244743]

Sequence

>retro_mmul_372
ATGTCAGAGCTGGCAGTGCAGAAGGCAGTGGTCCACCTTCCGGTGCTGCTCAGTGTGGTGGATCGTTTCAACTGAATCAG
CAAGGTTGGAAACCAGAAGTGCACTGTTGGTGTGCTTTTGGGGTCATGGCAGACAAAAGTACTTGATGTATCCAACAGTT
CTGGAATCCCTTTTGATGAAGATGACAAAGATAATTCTGTCTGGTTTTTAGACCATGATTATTTGGAAAACGTATGGAAT
GTTTGAGAAAATTAATGCCAAAGAATAGTTCGGTGGTACCACACAGGCCCTAAACTACACAAGAATGACATTGCCATCAA
TGAACTCATGAAAAGACACTACCCTAACTCAGTATTGGTATTACTGACTGAAACTAAAGGATCTGGGGCTGCCCACAGAA
GCATATATTTCAGTGAGAGAAGTCCATGATGATGGCACTCCAACCTCAAAAACATTTGAGTATGCGACTAGCGAAACTGG
AGCAGAGGAAGCTGAAGCAGCTGGAGCTGAACACTTGTTACAAGACATCAAAGAGGCTACAGTAGACAGTCTTTCCCAGC
TGATCACAAAGAAGTCCATGGTTGAGGAGACTGAACTCCAAGCTTTTGGGTATTAGGAGCTACCTGGAAAAAACAGCCAC
AGGCAAGCTGCCAATCAACCACCAGATCATT

Alignment

ORF - retro_mmul_372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.78 %
• Parental protein coverage: 70.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFL
          M.ELAVQK.VVH..VLLSVVD.FN.I.KVGNQK..VGVLLGSWQ.KVLDVSNS...PFDEDDKD.SVWFL
Retrocopy MSELAVQKAVVHLPVLLSVVDRFN*ISKVGNQKCTVGVLLGSWQTKVLDVSNSSGIPFDEDDKDNSVWFL

Parental  DHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKDLG-LPTEAYI
          DHDYLEN........N...RIV.WYHTGPKLHKNDIAINELMKR..PNSVLV......K..G.LPTEAYI
Retrocopy DHDYLENVWNV*E--N*CQRIVRWYHTGPKLHKNDIAINELMKRHYPNSVLVLL-TETKGSG>LPTEAYI

Parental  SVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRIT-NQVHG-LKGLNSKLLD
          SV.EVHDDGTPTSKTFE..TSE.GAEEAE..G.EHLL.DIK..TV..LSQ.IT...VHG.L..LNSKLL.
Retrocopy SVREVHDDGTPTSKTFEYATSETGAEEAEAAGAEHLLQDIKEATVDSLSQLIT<KEVHG<LRRLNSKLLG

Parental  IRSYLEKVATGKLPINHQII
          IRSYLEK.ATGKLPINHQII
Retrocopy IRSYLEKTATGKLPINHQII

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	0.11 RPM	37.42 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	40.62 RPM
SRP007412_cerebellum	0.06 RPM	31.00 RPM
SRP007412_heart	0.00 RPM	26.68 RPM
SRP007412_kidney	0.00 RPM	28.87 RPM
SRP007412_liver	0.00 RPM	26.56 RPM
SRP007412_testis	0.04 RPM	46.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_372 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_372 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_2910

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520, retro_cjac_2910,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372 , retro_mmul_417, retro_mmul_566,
Macaca mulatta	ENSMMUG00000013440	1 retrocopy	retro_mmul_387,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412,
Nomascus leucogenys	ENSNLEG00000005608	1 retrocopy	retro_nleu_1310,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205,
Tupaia belangeri	ENSTBEG00000016950	1 retrocopy	retro_tbel_4135,