RetrogeneDB ID: retro_mmul_401

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:108266806..108267267(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2568
• Ensembl ID: ENSMMUG00000023694
• Aliases: None
• Description: cyclin-dependent kinase 4 [Source:RefSeq peptide;Acc:NP_001248276]

Sequence

>retro_mmul_401
GCTGAGACCATCAAGGATCTGATGCACAAGTTTCAAAGAGACCTAGATTTTCTTCATTTCCATTGCATTGTTCACTGATA
TCTGAAGTCAGAGAACATTCCAGTGACAAGTGGTGGCACAGTCAAGCTGGCTGATTTAGTCTAGCTAGAATCTATAGCTA
CCAGATGGTGTTTATACCTGTGGTTGTTACACTCTTGTACTGTGCTCATGAGGTTCTTCTGCAATCTACACAGGCAACAT
CTGTGGACTTGTGAAGTGTTGGATGTGTCTTCGCAGAGATGTTTCCTCAAAAGCCTCTCTTCTGTGGAAACTCTAAAGCT
GAAAAGTTGGGCAAAATCTTTGACCTGATTGGGCTGCCTCTATAGGATGACGGGCCCTAAGATGTGTCTCTACCGCATGT
AGACTTTCTCCACAGAGGGCCTCATCCAGTAGAGTCGGTGGTGCCTGAGATGGAGCACAAC

Alignment

ORF - retro_mmul_401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.55 %
• Parental protein coverage: 50.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLAD-FGLARIYSYQMALTPVVVTLWYRA
          AETIKDLM..F.R.LDFLH..CIVH..LK.ENI.VTSGGTVKLAD.F.LARIYSYQM...PVVVTL.Y.A
Retrocopy AETIKDLMHKFQRDLDFLHFHCIVH*YLKSENIPVTSGGTVKLAD<FSLARIYSYQMVFIPVVVTLLYCA

Parental  PEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPPR
          .EVLLQST.AT.VD..SVGC.FAEMF..KPLFCGNS.A..LGKIFDLIGLP..DD.P.DVSLP...F..R
Retrocopy HEVLLQSTQATSVDL*SVGCVFAEMFPQKPLFCGNSKAEKLGKIFDLIGLPL*DDGP*DVSLPHVDFLHR

Parental  GPRPVQSVVPEMEES
          GP.PV.SVVPEME..
Retrocopy GPHPVESVVPEMEHN

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	11.32 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.20 RPM
SRP007412_cerebellum	0.00 RPM	18.60 RPM
SRP007412_heart	0.00 RPM	30.56 RPM
SRP007412_kidney	0.00 RPM	42.37 RPM
SRP007412_liver	0.00 RPM	26.09 RPM
SRP007412_testis	0.00 RPM	13.53 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_401 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_401 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_401 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_180
Gorilla gorilla	retro_ggor_275

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401 ,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,