RetrogeneDB ID: retro_mmul_1254

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:30680360..30680737(-)
• Located in intron of: ENSMMUG00000005551

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB38
• Ensembl ID: ENSMMUG00000016006
• Aliases: None
• Description: None

Sequence

>retro_mmul_1254
GTGAATTGTGCACTGAAGGAGCTCCACTGGGACTCAGAGGCCTTGGCGCACCTGCAGCTGTGGAACATTGCAATGAGGAA
AGATTGGGGAAATGACAAGAACCTGTTGTCTGGAATTTATAGGTGCATTGATTGTCTTCAGTATCACCAGGCCAGCCCCA
TTTGAAGCACAGTCAAAGTGGAAAAATGATTTGGACTAAATGTTAACTCATGGCAGATCAGTTTCTGTGGTTCTGCTGGC
CAAGAAATGTGACCGCGGGAGGGTGAATGCAGAAACTGTAGCCTCAAGATAGGCCAGATCTACATGGAACATAGTTTTGT
AGGATGAGTTGAAACATCAGCAAAGGAAAATGTGAACTTGATGAAGCCTCCAGGTGC

Alignment

ORF - retro_mmul_1254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.65 %
• Parental protein coverage: 61.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VDFALKVLHWDPETVVRLQLWDIA-GQERFGN-MTRVYYREAMGAFIVFDVTRPATFEAVAKWKNDLDSK
          V..ALK.LHWD.E....LQLW.IA...ER.G..MTR....E..GA.IVF..TRPA.FEA..KWKNDLD..
Retrocopy VNCALKELHWDSEALAHLQLWNIA<NEERLGK<MTRTCCLEFIGALIVFSITRPAPFEAQSKWKNDLD*M

Parental  LTLPNGKPVSVVLLANKCDQGK-DVLMNNGLKMDQFCKEHGFVGWFETSAKENIN-IDEASRC
          LT...G..VSVVLLA.KCD.G......N..LK..Q...EH.FVG..ETSAKEN.N..DEASRC
Retrocopy LT--HGRSVSVVLLAKKCDRGR<GECRNCSLKIGQIYMEHSFVG*VETSAKENVN<LDEASRC

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	0.11 RPM	0.11 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	0.32 RPM
SRP007412_cerebellum	0.00 RPM	0.26 RPM
SRP007412_heart	0.24 RPM	0.35 RPM
SRP007412_kidney	0.35 RPM	3.17 RPM
SRP007412_liver	0.04 RPM	0.00 RPM
SRP007412_testis	0.11 RPM	0.34 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1254 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000016006	1 retrocopy	retro_mmul_1254 ,
Pongo abelii	ENSPPYG00000003752	1 retrocopy	retro_pabe_1495,