RetrogeneDB ID: retro_mmul_1347

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:19824725..19825379(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000014937
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.10143
• Ensembl ID: ENSMMUG00000031106
• Aliases: None
• Description: ubiquitin fusion degradation protein 1 homolog [Source:RefSeq peptide;Acc:NP_001244660]

Sequence

>retro_mmul_1347
ATCTGCTACCTCTCACACTGGATGATGCAGAACTTGCTCTTGGAAGAAGGCAGCCTGGTCCAGGTGGAGAGTGTCAACCT
TCAAGTGGCCACCTACTGCAAATTCCAGCCTCAGAGCCATGACGTCCCGGACATCACCAACCCCAAAGCCGTATTAGAAA
ACACAGTTAGGAACTTTTCCTGTCTGACCACTGGGGATGTGATTGCCATCAACTATAATGAAAAGATCTACAAACTCGAA
CTGTGTGTGATGGAAACCAAACCTGACAAGGCAGTGTTCATCACTGAGTGTGACATGAACATGGACTTTGATGCTCCCCT
GGGCTACAAAGAACCTGAAAGACAAGTCCAGCATGAGAAGTCGACAGAAGGTGAAGCCTATCACAGTAGCTATGCTGGGG
AGCTGGGCTTCCGCGCCTTCTCCGGCTCTGGCAATAGACTGTATGGAAAGAAGAAAGGGGTGGAGCCCAGTCCTTCCCCA
GTCAAGCCTGGAGATATTAAAAGAGGAATTCCCAATTATGAATTTAAACTTGGTAAGATAACTTTCATCAGAAATGCGCG
TCTCCTTGTCAAAAAGGTTGAAGAGGATGAAGCTGGAGGCAGATTCGTCACTTTCTCTGGAGGACAGTTGTTGCATAAAA
AGGGAAGAAAGCCC

Alignment

ORF - retro_mmul_1347 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.13 %
• Parental protein coverage: 70.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAI
          ICYL.HWMMQNLLLEEG.LVQVESVNLQVATY.KFQPQS.D..DITNPKAVLEN..RNF.CLTTGDVIAI
Retrocopy ICYLSHWMMQNLLLEEGSLVQVESVNLQVATYCKFQPQSHDVPDITNPKAVLENTVRNFSCLTTGDVIAI

Parental  NYNEKIY--ELRVMETKPDKAVSIIECDMNVDFDAPLGYKEPERQVQHEESTEGEAGHSGYAGELGFRAF
          NYNEKIY..EL.VMETKPDKAV.I.ECDMN.DFDAPLGYKEPERQVQHE.STEGEA.HS.YAGELGFRAF
Retrocopy NYNEKIYKLELCVMETKPDKAVFITECDMNMDFDAPLGYKEPERQVQHEKSTEGEAYHSSYAGELGFRAF

Parental  SGSGNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQ
          SGSGNRL.GKKKGVEPSPSP.KPGDIKRGIPNYEFKLGKITFIRN.R.LVKKVEEDEAGGRFV.FSG.GQ
Retrocopy SGSGNRLYGKKKGVEPSPSPVKPGDIKRGIPNYEFKLGKITFIRNARLLVKKVEEDEAGGRFVTFSG-GQ

Parental  SLRKKGRKP
          .L.KKGRKP
Retrocopy LLHKKGRKP

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	20.84 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	21.66 RPM
SRP007412_cerebellum	0.00 RPM	28.86 RPM
SRP007412_heart	0.00 RPM	18.37 RPM
SRP007412_kidney	0.00 RPM	29.34 RPM
SRP007412_liver	0.00 RPM	18.84 RPM
SRP007412_testis	0.00 RPM	60.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1347 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1347 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1929
Gorilla gorilla	retro_ggor_175
Pongo abelii	retro_pabe_1593

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000004294	1 retrocopy	retro_fcat_604,
Homo sapiens	ENSG00000070010	1 retrocopy	retro_hsap_1929,
Gorilla gorilla	ENSGGOG00000004104	1 retrocopy	retro_ggor_175,
Myotis lucifugus	ENSMLUG00000002466	1 retrocopy	retro_mluc_1244,
Macaca mulatta	ENSMMUG00000031106	1 retrocopy	retro_mmul_1347 ,
Pongo abelii	ENSPPYG00000011580	1 retrocopy	retro_pabe_1593,
Pteropus vampyrus	ENSPVAG00000006417	1 retrocopy	retro_pvam_1349,