RetrogeneDB ID: retro_mmul_1025

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:52123108..52123544(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC12
• Ensembl ID: ENSMMUG00000019810
• Aliases: None
• Description: None

Sequence

>retro_mmul_1025
AAAGAACAGCTGAACGCCTTAAAGAAAACCAGGTACAGGGACAAGGAAAACGGGGAGCCAAAGACCAAGCAGCTCAGAGA
AGAGGAGGAGGAAAGCAAGAAGCTCAGGAAATTCAGTCTACAGAACCATGTTCCAAAGGATGAGGACCTGAAAAGGAGGA
GGGTTTCCAGGGCAAACCAGTTGCAGTAGAGGAGAAGATGAAGGAGAAGCTGTAGGCCGCCAAGGCACAGCCTGTCACTG
AGGAGATGGACCTGGTCAACCTTGCACTCTAGAAGCCTGATTGCGACCTAAGAGAGATGTGAGCAAGAACCTGGAGAAAC
TAAACAAAAAGACTCAGAGGACCATTGCTGAGCTGAGCCGTGGGAGGCTAAAAGGCCCAATTGACAGCCTAGTCTCTGCA
GTGGAAGCCACCACTGAACAAGAGGCCTGTGACAAC

Alignment

ORF - retro_mmul_1025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.11 %
• Parental protein coverage: 88.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KERLKALREKTGRKDKEDGEPRTKHLREEEEEGEKHRELRLRNYVPEDEDLKKRRVP-QAKPVAVEEKVK
          KE.L.AL..KT...DKE.GEP.TK.LREEEEE..K.R...L.N.VP.DEDLK.RRV..Q.KPVAVEEK.K
Retrocopy KEQLNALK-KTRYRDKENGEPKTKQLREEEEESKKLRKFSLQNHVPKDEDLKRRRVS<QGKPVAVEEKMK

Parental  EQLEAAKPEPVIEEVDLANLAPRKPDWDL-KRDVAKKLEKLKKRTQRAIAELIRERLKGQDDSLASAVDA
          E.L.AAK..PV.EE.DL.NLA..KPD.DL.KRDV.K.LEKL.K.TQR.IAEL.R.RLKG..DSL.SAV.A
Retrocopy EKL*AAKAQPVTEEMDLVNLAL*KPDCDL<KRDVSKNLEKLNKKTQRTIAELSRGRLKGPIDSLVSAVEA

Parental  ATEQKACDS
          .TEQ.ACD.
Retrocopy TTEQEACDN

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	8.74 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	17.37 RPM
SRP007412_cerebellum	0.00 RPM	8.07 RPM
SRP007412_heart	0.00 RPM	13.78 RPM
SRP007412_kidney	0.00 RPM	13.15 RPM
SRP007412_liver	0.00 RPM	11.72 RPM
SRP007412_testis	0.00 RPM	4.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1025 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1025 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1025 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2257
Pan troglodytes	retro_ptro_1597
Pongo abelii	retro_pabe_1957

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002280	3 retrocopies	retro_cjac_1212, retro_cjac_2317, retro_cjac_3225,
Dipodomys ordii	ENSDORG00000016567	1 retrocopy	retro_dord_303,
Echinops telfairi	ENSETEG00000000030	2 retrocopies	retro_etel_1445, retro_etel_2038,
Homo sapiens	ENSG00000160799	1 retrocopy	retro_hsap_2257,
Macaca mulatta	ENSMMUG00000019810	1 retrocopy	retro_mmul_1025 ,
Mus musculus	ENSMUSG00000019659	1 retrocopy	retro_mmus_1275,
Nomascus leucogenys	ENSNLEG00000006219	1 retrocopy	retro_nleu_1282,
Ochotona princeps	ENSOPRG00000005086	1 retrocopy	retro_opri_746,
Pongo abelii	ENSPPYG00000013924	2 retrocopies	retro_pabe_1957, retro_pabe_2033,
Pan troglodytes	ENSPTRG00000014862	1 retrocopy	retro_ptro_1597,
Sarcophilus harrisii	ENSSHAG00000003265	1 retrocopy	retro_shar_251,