RetrogeneDB ID: retro_mmul_1242

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:61584807..61585666(+)
• Located in intron of: None

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_1242
ATGCCAGAGCTGGTGAAGGTGCAGAAGCTGGTGGTCCACCGCCTGGTGCTGCTCAGTGTGGTGGATCATTTCAACCAAAT
CGGCAAGGCTGGAAACCAGAAGTAAGTTGTTGGTGTGCTTTTGGGGTCATGGCAAAAGAAAGTACTTGATATATCAAACA
GTGTGCAGTTCCTTTTGATGAAGATGACAAAGACAATTCTGTGTGGTTTTTAGACCATGATTATTTGGAAAACGTGTATG
GAATGTTTAAGAAAAGTCAATGCCAGAGAAAGAATAGTTGGCTGGTACCACACAGGCCCTAAAATACACATGAATGACAT
TACCATCAATGAACTCATGAAAAGATACTATCCTAACTCGGTATTGGGTCATTATTGACGTGAATCCAAAGGACCTAGAG
TTGCCCACAGAAGCGTACGTTTCAGTGGAAGAAGTCCGTGATGATGGAACTCCAACCTTGAAAACATTTGAACACGTGAC
CAGTGAAATTGGAGCAGAGTAAGCTGAGGAAGTTGGAGTTGAACACTTGTTACAGGACATCAAAGACACGACGGTGGGCG
CTCTGTCCCAGCGGATCACAAATCAGGTCCATGGTTTGAAGGGACTGAACTCCAAGCTTCTGGATATCAGGAGCTACCTG
GAAGAAGTAGCCACAGGCAAGCTGCCCATCCACCACCAGATCATCTACGAGCTGCAGGACATCTTCAGCCTGCTGCCAGA
CATGAGCCTGCAGGAGCCTCTTAAGGCCTTTTACCTGAGGACCAAGGACCAGATGGTGGTAGTGTACTCGGCCTCACTGA
TCCATTCTGTGGTTGCTCTGCACAACCTCATCAACAAGATTGCCAACCAGGATGGAGAC

Alignment

ORF - retro_mmul_1242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.52 %
• Parental protein coverage: 88.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPELA-VQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSF-AVPFDEDDKDDSVW
          MPEL..VQK.VVH.LVLLSVVDHFN.IGK.GNQK.VVGVLLGSWQKKVLD.SNS..AVPFDEDDKD.SVW
Retrocopy MPELVKVQKLVVHRLVLLSVVDHFNQIGKAGNQK*VVGVLLGSWQKKVLDISNSV<AVPFDEDDKDNSVW

Parental  FLDHDYLENMYGMFKK-VNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVL-VIIDVKPKDLGLPTE
          FLDHDYLEN.YGMFKK.VNARERIVGWYHTGPK.H.NDI.INELMKRY.PNSVL.VIIDV.PKDL.LPTE
Retrocopy FLDHDYLENVYGMFKK>VNARERIVGWYHTGPKIHMNDITINELMKRYYPNSVL>VIIDVNPKDLELPTE

Parental  AYISVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRITNQVHGLKGLNSKLL
          AY.SVEEV.DDGTPT.KTFEHVTSEIGAE.AEEVGVEHLL.DIKDTTVG.LSQRITNQVHGLKGLNSKLL
Retrocopy AYVSVEEVRDDGTPTLKTFEHVTSEIGAE*AEEVGVEHLLQDIKDTTVGALSQRITNQVHGLKGLNSKLL

Parental  DIRSYLEKVATGKLPINHQIIYQLQDVFNLLPDVSLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLI
          DIRSYLE.VATGKLPI.HQIIY.LQD.F.LLPD.SLQE..KAFYL.T.DQMVVVY.ASLI.SVVALHNLI
Retrocopy DIRSYLEEVATGKLPIHHQIIYELQDIFSLLPDMSLQEPLKAFYLRTKDQMVVVYSASLIHSVVALHNLI

Parental  NNKIANRDAE
          .NKIAN.D..
Retrocopy -NKIANQDGD

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	37.42 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	40.62 RPM
SRP007412_cerebellum	0.00 RPM	31.00 RPM
SRP007412_heart	0.00 RPM	26.68 RPM
SRP007412_kidney	0.00 RPM	28.87 RPM
SRP007412_liver	0.51 RPM	26.56 RPM
SRP007412_testis	0.00 RPM	46.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1242 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1242 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1242 has 0 orthologous retrocopies within eutheria group .

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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,