RetrogeneDB ID: retro_mmul_387

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:91344093..91345072(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS6
• Ensembl ID: ENSMMUG00000013440
• Aliases: None
• Description: COP9 signalosome subunit 6 [Source:HGNC Symbol;Acc:21749]

Sequence

>retro_mmul_387
ATGGCGGCGGCGGCGGCGGCTGCAGCTACAAACGGGAGCAGAGGGAGCAGCGGGACGGAGGTGGATGCAGCAGTAGTTCC
CAGCGTGATGCCCTCTGGAGTGACTGGGAGTGTTTCCGTCGCTCTCCATCCCCTTGTCATTCTCAACATCTCTGACTACT
GGATCTGCATGCGCTCCCAGGAGGGGCGGCCTGTGCAAGTGACTGGGGCTTTGATTGGCAAGCAGGAAGGCCGAAATATC
GAGGTGATGAACTACTTTGAGCTGCTGTCCCACACCGTGGAAGAGAAGATTATCATTGACAAGGAATATTATTACACCAA
GGAGGAGCAGTTTAAACAGGTGTTCAAGGAGCTGGAGTTTCTGGGTTAGTATACCACAGGGGGGCCACCTGACCCCTCGG
ACATCCACGTCCATAAGCAGGTGTGTGAGATCATCGAGAGCCCCCTCTTTCTGAAGCCGAACCCTATGACCAAGCACACA
GATCTTCCTGTCAGCGTTTTTGAGTCTGCCATCGATATAATCAAGGGAGAGGCCACAATGCTGTTTGCTGAGCTGACCTA
CACTCTGGCCACAGAGGAAGCGGGAACGCATTGGTGTAGACCACGTAGCCCGAATGACAGCAACAGGTAGTGGAGAGAAC
TCCACTGTGGCCGAACACCTGATAGCACAGCACAGCGCCATCAAGATGCTGCACAGCCGCGTCAAGCTCATCTTGGAGTA
CGTCAAGGCCTCTGAAGCAGGAGAGGTCCCCTTTAATCATGAGATCCTGCGGGAGGCCTATGCTCTGTGTCACTGCCTTC
CGGTGCTCAGCACAGACAAGTTCAAGACAGATTTTTATGATCAATGCAACGACGTGGGGCTCATGGCCTACCTCGGCACC
ATCACCAAAACGTGTAACACCATGAACCAGTTTGTGAACAAGTTCAACGTCCTCTACGATCGACAAGGCATAGGCAAGCG
AATGCGCAGGCTCTTCTTC

Alignment

ORF - retro_mmul_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAAAGAATNGTGGSSGMEVDAAVVPSVMASGVTGSVSVALHPLVILNISDHWIRMRSQEGRPVQVIGA
          MAAAAA.AATNG..GSSG.EVDAAVVPSVM.SGVTGSVSVALHPLVILNISD.WI.MRSQEGRPVQV.GA
Retrocopy MAAAAAAAATNGSRGSSGTEVDAAVVPSVMPSGVTGSVSVALHPLVILNISDYWICMRSQEGRPVQVTGA

Parental  LIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELEFLGWYTTGGPPDPSDIHVHKQ
          LIGKQEGRNIEVMN.FELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELEFLG.YTTGGPPDPSDIHVHKQ
Retrocopy LIGKQEGRNIEVMNYFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELEFLG*YTTGGPPDPSDIHVHKQ

Parental  VCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEATMLFAELTYTLATEEA-ERIGVDHVARMTATG
          VCEIIESPLFLK.NPMTKHTDLPVSVFES.IDII.GEATMLFAELTYTLATEEA.ERIGVDHVARMTATG
Retrocopy VCEIIESPLFLKPNPMTKHTDLPVSVFESAIDIIKGEATMLFAELTYTLATEEA>ERIGVDHVARMTATG

Parental  SGENSTVAEHLIAQHSAIKMLHSRVKLILEYVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFY
          SGENSTVAEHLIAQHSAIKMLHSRVKLILEYVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFY
Retrocopy SGENSTVAEHLIAQHSAIKMLHSRVKLILEYVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFY

Parental  DQCNDVGLMAYLGTITKTCNTMNQFVNKFNVLYDRQGIGRRMRGLFF
          DQCNDVGLMAYLGTITKTCNTMNQFVNKFNVLYDRQGIG.RMR.LFF
Retrocopy DQCNDVGLMAYLGTITKTCNTMNQFVNKFNVLYDRQGIGKRMRRLFF

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	75.41 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	106.78 RPM
SRP007412_cerebellum	0.26 RPM	67.48 RPM
SRP007412_heart	0.06 RPM	55.65 RPM
SRP007412_kidney	0.00 RPM	59.62 RPM
SRP007412_liver	0.08 RPM	51.78 RPM
SRP007412_testis	0.11 RPM	140.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_387 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_387 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014814	1 retrocopy	retro_cfam_1389,
Felis catus	ENSFCAG00000003561	1 retrocopy	retro_fcat_522,
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,
Monodelphis domestica	ENSMODG00000004170	1 retrocopy	retro_mdom_220,
Otolemur garnettii	ENSOGAG00000016843	1 retrocopy	retro_ogar_1236,
Pteropus vampyrus	ENSPVAG00000005186	1 retrocopy	retro_pvam_690,