RetrogeneDB ID: retro_mmul_2110

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:123505312..123506138(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000003033
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4582
• Ensembl ID: ENSMMUG00000016239
• Aliases: None
• Description: None

Sequence

>retro_mmul_2110
CAGTATACAGCGTACAGTTTCTTCACTAAATTGACGGCAGTTGAGCTGTGGAAAGGTACTTTGGCAGGGACTGGTACTGG
AGCAAGAAAAGGAAGAGGCAAAAGAACTAAAAAGAAGAAAGGAAAGGATCTGAACCGGGGTCTGATCATTGGTGAAGGGC
GTTACTGTTTTCTGTGGCCTGATCTGAATGTCCCTCTTCTGAAAAATGGAGCAGTGCAAACCATTGCCCAAAGACGCAAG
GAAGAGCGGGAGAAGGTGGAGGCGGACATGATCCAGCAGAGAGAAGAGTGGGGCCTAAAGAGGAAGATGAAGGTTAAACG
GGAGCCAGGATGGAGTGGAAACTCATGGAGAGGCGTCAGTCTTGGCCTGCCTGACCCTGGTCCCAGTGGAGAAACATATG
AGGATTTTGATACCAGGATACTTGAGGTAAGAAATGTTTTCAATATGACAGCAGAAAGAGGGAAGAAAGAAATCGGTCCA
TGTCCTGGTGGCTGTGGGGAACAGAAAAGGAGCTGCAGGTTTTGCTGTTGCGAAAACCATTGAACGGGTGGTTTTTAGGA
AAGCAAAGAACAGAGCAGTTCACTATCTGCATTATATAGAACAATATGAAGACCCTACAATATTCCATGATATTTCATTA
AGATGTAAAAGGACACGTATCAAGATGAAGAAACAACCCAAAGGTTATGGCCTCTACTGCCACAGGGCCATCATTACCAT
CTGCAGGCTCACTGGCATCAACGACATGTATGCCAAGGTCTCTGGGTCTGTCAGTAGGCTCAGCCTTACCTGGGGCCTCT
TCCGTGGGCTCTCCAGACAGAAAACC

Alignment

ORF - retro_mmul_2110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.06 %
• Parental protein coverage: 77.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QYRPYSFFTKLTADELWKGALAESGAGSRKGRGKRTKKRKRKDLNRGQIIGEGHYGFLWPGLNVPLMKNG
          QY..YSFFTKLTA.ELWKG.LA..G.G.RKGRGKRTKK.K.KDLNRG.IIGEG.Y.FLWP.LNVPL.KNG
Retrocopy QYTAYSFFTKLTAVELWKGTLAGTGTGARKGRGKRTKKKKGKDLNRGLIIGEGRYCFLWPDLNVPLLKNG

Parental  AVQTIAQRSKEEQKKMEADMIQQREEWYRKRKIKVKHERGWTGNSWGGVSLGPPGPGPNGETYEDFDTRV
          AVQTIAQR.KEE..K.EADMIQQREEW..KRK.KVK.E.GW.GNSW.GVSLG.P.PGP.GETYEDFDTR.
Retrocopy AVQTIAQRRKEEREKVEADMIQQREEWGLKRKMKVKREPGWSGNSWRGVSLGLPDPGPSGETYEDFDTRI

Parental  LEVRNVFNMTA-KEGRKKSVRVLVAVGNGKGAAGFAIGKATDRMDAFRKAKNRALYCLHYIERYEDHTIF
          LEVRNVFNMTA.KEGRKKSV.VLVAVGN.KGAAGFA..K...R...FRKAKNRA...LHYIE.YED.TIF
Retrocopy LEVRNVFNMTA>KEGRKKSVHVLVAVGNRKGAAGFAVAKTIERV-VFRKAKNRAVHYLHYIEQYEDPTIF

Parental  HDISLRFKRTRIRMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSVNMINLTRGLFYGLSRQVT
          HDISLR.KRTRI.MKKQPKGYGL.CHRAIITICRL.GI.DMYAKVSGSV....LT.GLF.GLSRQ.T
Retrocopy HDISLRCKRTRIKMKKQPKGYGLYCHRAIITICRLTGINDMYAKVSGSVSRLSLTWGLFRGLSRQKT

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	18.04 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	27.21 RPM
SRP007412_cerebellum	0.00 RPM	12.53 RPM
SRP007412_heart	0.00 RPM	37.27 RPM
SRP007412_kidney	0.00 RPM	21.13 RPM
SRP007412_liver	0.00 RPM	13.02 RPM
SRP007412_testis	0.00 RPM	26.42 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2110 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2110 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009757	1 retrocopy	retro_amel_1242,
Callithrix jacchus	ENSCJAG00000018942	1 retrocopy	retro_cjac_2129,
Homo sapiens	ENSG00000144029	1 retrocopy	retro_hsap_3116,
Gorilla gorilla	ENSGGOG00000001750	1 retrocopy	retro_ggor_2139,
Microcebus murinus	ENSMICG00000007318	1 retrocopy	retro_mmur_565,
Myotis lucifugus	ENSMLUG00000003183	1 retrocopy	retro_mluc_2245,
Macaca mulatta	ENSMMUG00000016239	2 retrocopies	retro_mmul_2110 , retro_mmul_2251,
Mus musculus	ENSMUSG00000027374	1 retrocopy	retro_mmus_2014,
Nomascus leucogenys	ENSNLEG00000000002	1 retrocopy	retro_nleu_1438,
Pongo abelii	ENSPPYG00000012051	1 retrocopy	retro_pabe_2574,
Pan troglodytes	ENSPTRG00000012209	1 retrocopy	retro_ptro_2107,