RetrogeneDB ID: retro_mmul_2236

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:70468030..70468258(-)
• Located in intron of: ENSMMUG00000019526

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEDD8
• Ensembl ID: ENSMMUG00000029409
• Aliases: None
• Description: NEDD8 [Source:RefSeq peptide;Acc:NP_001253817]

Sequence

>retro_mmul_2236
CAGACGCTGACCGGAAAGGAGACTGAGATTGACACTGAACCTACAGACAAGGTGTAGCGGATCAAGGAGCGTGTGGAGGA
GAAAGAGGGAATCCCCCCACAACAGCAGAGGCTCATCTACAGTGGCAAACAAACGAATGATGAGAAGACAGCAGCTGATT
ACAAGATTTTAGGTGGTTCAGTTCTTCACCTGGTGTTGGCTCTGAGAGGAGGAGGTGGTCTTAGGCAG

Alignment

ORF - retro_mmul_2236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.42 %
• Parental protein coverage: 93.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRG
          .TLTGKE.EID.EPTDKV.RIKERVEEKEGIPPQQQRLIYSGKQ.NDEKTAADYKILGGSVLHLVLALRG
Retrocopy QTLTGKETEIDTEPTDKV*RIKERVEEKEGIPPQQQRLIYSGKQTNDEKTAADYKILGGSVLHLVLALRG

Parental  GGGLRQ
          GGGLRQ
Retrocopy GGGLRQ

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	4.15 RPM	51.88 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	76.32 RPM
SRP007412_cerebellum	3.62 RPM	32.93 RPM
SRP007412_heart	2.94 RPM	40.34 RPM
SRP007412_kidney	3.99 RPM	35.68 RPM
SRP007412_liver	2.73 RPM	24.50 RPM
SRP007412_testis	3.05 RPM	35.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2236 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2236 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064,
Erinaceus europaeus	ENSEEUG00000011640	2 retrocopies	retro_eeur_165, retro_eeur_43,
Echinops telfairi	ENSETEG00000018391	2 retrocopies	retro_etel_1118, retro_etel_1677,
Homo sapiens	ENSG00000129559	1 retrocopy	retro_hsap_180,
Macaca mulatta	ENSMMUG00000029409	1 retrocopy	retro_mmul_2236 ,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681,
Vicugna pacos	ENSVPAG00000009104	4 retrocopies	retro_vpac_270, retro_vpac_316, retro_vpac_480, retro_vpac_558,