RetrogeneDB ID: retro_mmul_1748

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:7907427..7909076(+)
• Located in intron of: ENSMMUG00000029993

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3165
• Ensembl ID: ENSMMUG00000005228
• Aliases: None
• Description: 26S proteasome non-ATPase regulatory subunit 4 [Source:RefSeq peptide;Acc:NP_001130040]

Sequence

>retro_mmul_1748
ATGGCGTCCGCCTCCTCCCAGCCGTCGTTGGCGGTCGGTTTTCCATCCTTGGATCCCGGAGTCCCTTCCTGTACCGTGTC
CTCAGCGTCTGGAATCAAGAGCCCCATGGCATCCGAGGTGCTTTATGCCTCTGGCATGCCCATCAAGAAAACAGGCCATC
GAGGTGTCGATTCCTCAGGAGAGACAACATATAAAAAGACACCCTCATCAGCCTTGAAAGGTGCCATCCAGTTAGGCATC
ACTCACACAGTGGGGAGCCTGAGTACCAAACCGGAGCGTGATGTCCTCATGCAAGATTTCTACGTGGTGGAGAGTATCTT
CTTCCCCAGTGAAGGGAGCAAGCTGACCCCTGCTCATCACTACAACGACTTTCGTTTCAAGACCTATGCACCTGTTGCCT
TCCGCTACTTTCGGGAGCTATTTGGTATTCCGCCGGATGATTACTTGTGCTCCCTCTGCAGTGAGCCGCTGATTGAACTC
TGTAGCTCTGGAGCTAGTGGTTCCCTGTTCTATGTGTCCAGCGACGATGACTTCATTATTAAGACAGTCCAACATAAAGA
GGCGGAGTTTCTGCAGAAGCTGCTTCCAGGATACTACTTGAACCTCAACCAGAACCCTCGGACTTTGTTGCCTAAATTCT
ATGGACTGTACTGTGTGCAGGCAGGTGGCAAGAACATTCGGATTGTGGTGATGAACAATCTTTTACCAAGATCAGTCAAA
ATGCATACCAAATATGACCTCAAAGGCTCAACCTACAAACGCCGGGCTTCCCAGAAAGAGCGAGAGAAGCCTCTTCCCAC
ATTTAAAGACCTAGACTTCTTACAAGACATCCCTGATGGTCTTTTTTTGGATGCTGACATGTACAATGCTCTCTGTAAGA
CCCTGCAGCGTGACTGTTTGGTGCTGCAGAGCTTCAAGATAATGGACTATAGCCTCTTGCTGTCAATCCACAATATAGAT
TATGCACAACGAGAGCCCTTAAGCAGCGACACCCTTCAAGTGTCCGTTGACACTCAAAGACTGACCCCCCAAAAGGTTCT
GTACTCCACAGCCATGGAATCCATCCAGGGAGAGGCTCGCCTGGGCGACACCATGGAGACCGATGACCATATGGGTGGCA
TCCCTGCTCAGACTAGTAAAGGCGAAAGGCTTCTGCTTTATATTGGCATCATTGACATTCTACAGTCTTACACATGTCTT
AAGAAGTTGGAGCACTCTTGGAAAGCCCTGGTACATGACGGGGACACTGTCTCAGTGCACAACCCAGGCTTCTATGCTGA
ACGGTTCCAGCGCTTCATGTGCAACGCAGTATTTAAGAAGATCCCCTTGAAGCCTTCTCCTTCCAAAAAGTTTGGGACTG
GCTCATCTTTCTCCCGGCGTACGGGCTCCAGTGGCAACTCCTGCATTACTTACCAGCCACTGGTCTCTGGGGAACACAAG
GCACAGGTGACAACAAAGGCAGAAGTGGAGCCAGGTGTTCACCTTGGTCGTCCTGATGTTTTACCGTAGAATCCTCCTTT
GGAGGAAATCAGTGAGGGCTCACCTATTACTGAGTCCAGTTTCTCACCTGTAGTTGGAGAGACTTTGCGTATGCTAACTA
CAAGTACAACCTTGGAAAACTTGAACGTGCAGAGTCAGAGTTCACCCAT

Alignment

ORF - retro_mmul_1748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASASSGPSSSVGFSSFDPAVPSCTSSSASGIKRPVAPEVPYASGMPIKKIGHRSVDSSGETTYKKTTSS
          MASASS.PS..VGF.S.DP.VPSCT.SSASGIK.P.A.EV.YASGMPIKK.GHR.VDSSGETTYKKT.SS
Retrocopy MASASSQPSLAVGFPSLDPGVPSCTVSSASGIKSPMASEVLYASGMPIKKTGHRGVDSSGETTYKKTPSS

Parental  ALKGAIQLGITHTVGSLSTKPERDVLMQDFYVVESIFFPSEGSNLTPAHHYNDFRFKTYAPVAFRYFREL
          ALKGAIQLGITHTVGSLSTKPERDVLMQDFYVVESIFFPSEGS.LTPAHHYNDFRFKTYAPVAFRYFREL
Retrocopy ALKGAIQLGITHTVGSLSTKPERDVLMQDFYVVESIFFPSEGSKLTPAHHYNDFRFKTYAPVAFRYFREL

Parental  FGIRPDDYLYSLCSEPLIELCSSGASGSLFYVSSDDEFIIKTVQHKEAEFLQKLLPGYYMNLNQNPRTLL
          FGI.PDDYL.SLCSEPLIELCSSGASGSLFYVSSDD.FIIKTVQHKEAEFLQKLLPGYY.NLNQNPRTLL
Retrocopy FGIPPDDYLCSLCSEPLIELCSSGASGSLFYVSSDDDFIIKTVQHKEAEFLQKLLPGYYLNLNQNPRTLL

Parental  PKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHIKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPDG
          PKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMH.KYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPDG
Retrocopy PKFYGLYCVQAGGKNIRIVVMNNLLPRSVKMHTKYDLKGSTYKRRASQKEREKPLPTFKDLDFLQDIPDG

Parental  LFLDADMYNALCKTLQRDCLVLQSFKIMDYSLLMSIHNIDHAQREPLSSET-QYSVDTRRPAPQKALYST
          LFLDADMYNALCKTLQRDCLVLQSFKIMDYSLL.SIHNID.AQREPLSS.T.Q.SVDT.R..PQK.LYST
Retrocopy LFLDADMYNALCKTLQRDCLVLQSFKIMDYSLLLSIHNIDYAQREPLSSDTLQVSVDTQRLTPQKVLYST

Parental  AMESIQGEARRGGTMETDDHMGGIPARNSKGERLLLYIGIIDILQSYRFVKKLEHSWKALVHDGDTVSVH
          AMESIQGEAR.G.TMETDDHMGGIPA..SKGERLLLYIGIIDILQSY...KKLEHSWKALVHDGDTVSVH
Retrocopy AMESIQGEARLGDTMETDDHMGGIPAQTSKGERLLLYIGIIDILQSYTCLKKLEHSWKALVHDGDTVSVH

Parental  RPGFYAERFQRFMCNTVFKKIPLKPSPSKKFRSGSSFSRRVGSSGNSCITYQPSVSGEHKAQVTTKAEVE
          .PGFYAERFQRFMCN.VFKKIPLKPSPSKKF..GSSFSRR.GSSGNSCITYQP.VSGEHKAQVTTKAEVE
Retrocopy NPGFYAERFQRFMCNAVFKKIPLKPSPSKKFGTGSSFSRRTGSSGNSCITYQPLVSGEHKAQVTTKAEVE

Parental  PGVHLGRPDVLPQTPPLEEISEGSPIPDPSFSPIVGETLQMLTTSTTLE-KLEVAESEFTH
          PGVHLGRPDVLP..PPLEEISEGSPI...SFSP.VGETL.MLTTSTTLE.KLE.AESEFTH
Retrocopy PGVHLGRPDVLP*NPPLEEISEGSPITESSFSPVVGETLRMLTTSTTLE<KLERAESEFTH

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	106.11 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	143.75 RPM
SRP007412_cerebellum	0.39 RPM	79.04 RPM
SRP007412_heart	0.12 RPM	105.52 RPM
SRP007412_kidney	0.00 RPM	76.64 RPM
SRP007412_liver	0.00 RPM	89.34 RPM
SRP007412_testis	5.99 RPM	311.88 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1748 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1748 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3420
Pan troglodytes	retro_ptro_2324

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143398	2 retrocopies	retro_hsap_3420, retro_hsap_716,
Macaca mulatta	ENSMMUG00000005228	1 retrocopy	retro_mmul_1748 ,
Nomascus leucogenys	ENSNLEG00000010130	2 retrocopies	retro_nleu_468, retro_nleu_5,
Otolemur garnettii	ENSOGAG00000002846	1 retrocopy	retro_ogar_1855,
Pongo abelii	ENSPPYG00000000872	4 retrocopies	retro_pabe_3037, retro_pabe_3112, retro_pabe_59, retro_pabe_619,
Pan troglodytes	ENSPTRG00000001282	2 retrocopies	retro_ptro_2324, retro_ptro_511,