RetrogeneDB ID: retro_mmul_489

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:47116197..47116521(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX3
• Ensembl ID: ENSMMUG00000021104
• Aliases: None
• Description: None

Sequence

>retro_mmul_489
AAAGTTAATGTCATAGATAGCCACTGGAGAGGTTCAAGGGAAGATATATCAATTTTGACAACTGAAGACAAAATTGTTTC
TTCGCTGGCAAAAATATTCAACTTTTAAGGAAAACAGAAATATAATGTTTATTGTGAATTTCCAGCCAAACAAAAGGCAG
ACACACTGGCTTTCACTGTTCTCTTTGAATAGAAGCTGCCTCCTCTAGCGCTTCACGCATTCTGGGTGGAAAGCAACAAT
TACTTTGCTGTGACAAAGCCATGGTGTTGGTTTGCTTCATTGATTCCTTTTCCCTTGGGTTTGATCCTGTCTGGAAAAAT
GTCT

Alignment

ORF - retro_mmul_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.59 %
• Parental protein coverage: 73.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVNVIDNTWRGSRGDVPILTTEDNMVSQPAKILNFLRKQKYNADYELSAKQGADTLAYIALLEEKLLPAV
          KVNVID..WRGSR.D..ILTTED..VS..AKI.NF..KQKYN...E..AKQ.ADTLA...L.E.KL.P..
Retrocopy KVNVIDSHWRGSREDISILTTEDKIVSSLAKIFNF*GKQKYNVYCEFPAKQKADTLAFTVLFE*KLPPLA

Parental  LHTFWVESDNYFTVTKP--WFASQIPFPLSLILPGRMS
          LH.FWVES.NYF.VTKP..WFAS.IPFPL.LIL.G.MS
Retrocopy LHAFWVESNNYFAVTKPWCWFASLIPFPLGLILSGKMS

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	1.79 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.51 RPM
SRP007412_cerebellum	0.00 RPM	2.32 RPM
SRP007412_heart	0.00 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.82 RPM
SRP007412_liver	0.00 RPM	0.16 RPM
SRP007412_testis	0.00 RPM	0.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_489 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_489 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010893	1 retrocopy	retro_chof_1828,
Callithrix jacchus	ENSCJAG00000019700	1 retrocopy	retro_cjac_2994,
Macaca mulatta	ENSMMUG00000010185	1 retrocopy	retro_mmul_1643,
Macaca mulatta	ENSMMUG00000021104	1 retrocopy	retro_mmul_489 ,
Vicugna pacos	ENSVPAG00000009404	1 retrocopy	retro_vpac_626,