RetrogeneDB ID: retro_mmul_1354

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:56798025..56798661(-)
• Located in intron of: ENSMMUG00000021184

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1686
• Ensembl ID: ENSMMUG00000016769
• Aliases: None
• Description: 26S protease regulatory subunit 8 [Source:RefSeq peptide;Acc:NP_001248230]

Sequence

>retro_mmul_1354
AGAACTGAAGAACTCCAGTCAGTTGTGAATGATAAGAGCCAATACCTCCAGAGGCTGCAGGCAGAAAGGAATGAACTAAA
TGCAAAAGTTCACCTATTGCAGGAGGAGCTGCAGCTGCTGCTGGAACAGGGCTCCTGTATGAGGGAAGTAGTCCGGGCCA
TGGATATGGAGAAAATGTTAGTCAAGGTATATCCCAAGGGCAAGTTTGTCTTAGGTGTGGACAGAAACAGCGACATCAAT
GACATGAGACCCAATTGCCAGGTGGCGCTCAGAAATGATAGCTACACACTGCACAACATCATACCCAACAAAGTAGACCC
ACTGGTGTCACCAGTGATGGTGGAGAAGGTGCCAGCCTTGATTTAAGAGATGATTGGTGGACTGGACAAGCAGATTAAAG
ACATCAGAGAAGTGATCGAACTGCCTGTTAAGCATCCCAAGCTCTTTGAAGCACTGGGTATCGCACAACCCAAGGTGGTC
CTGCTGTGTGGACCTCTAGGCACTGGGAAGACACTGTTTGCCTGGGTCATGGCTCATCATATAGACTGTACTTTTGTTCA
TATCCCTGGCTCTGAATTGGTACAGAAATTCATCACAGAAGGGCCAAGAATGGTGAGGGAGCTGTCTGTCATGGCA

Alignment

ORF - retro_mmul_1354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.94 %
• Parental protein coverage: 65.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLREELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFV
          ..EELQ..VNDKSQ.L.RLQA.RNELNAKV.LL.EELQLL.EQGS...EVVRAMD..K.LVKV.P.GKFV
Retrocopy RTEELQSVVNDKSQYLQRLQAERNELNAKVHLLQEELQLLLEQGSCMREVVRAMDMEKMLVKVYPKGKFV

Parental  VDVDKNIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIE
          ..VD.N.DIND..PNC.VALRNDSYTLH.I.PNKVDPLVS..MVEKVP....EMIGGLDKQIK.I.EVIE
Retrocopy LGVDRNSDINDMRPNCQVALRNDSYTLHNIIPNKVDPLVSPVMVEKVPALI*EMIGGLDKQIKDIREVIE

Parental  LPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFV
          LPVKHP.LFEALGIAQPK.VLL.GP.GTGKTL.A...AHH.DCTF....GSELVQKFI.EG.RMVREL.V
Retrocopy LPVKHPKLFEALGIAQPKVVLLCGPLGTGKTLFAWVMAHHIDCTFVHIPGSELVQKFITEGPRMVRELSV

Parental  MA
          MA
Retrocopy MA

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	0.34 RPM	127.29 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	143.35 RPM
SRP007412_cerebellum	0.13 RPM	152.07 RPM
SRP007412_heart	0.24 RPM	112.12 RPM
SRP007412_kidney	0.00 RPM	139.20 RPM
SRP007412_liver	0.12 RPM	110.00 RPM
SRP007412_testis	0.11 RPM	353.19 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1354 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1354 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1949
Gorilla gorilla	retro_ggor_1418

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354 ,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,