RetrogeneDB ID: retro_mmul_1507

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:40535513..40535756(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2AP1
• Ensembl ID: ENSMMUG00000000434
• Aliases: None
• Description: None

Sequence

>retro_mmul_1507
TCACAGTATCACCAGCTGCTGAGTGACTATAGGCCACCATCCCTAGGCTATACCCAGGGAACTGGAAACAGCCAAGTGAC
CCCAAAGCAGATGTGCTAAACTGCTGGCTATCATCCAAGAGCTGGGGGAGTGATCAGACCCACCTATACAGGGAGCAAGA
GCACAGTGAAGAGACCAAAACAAGTTACCATTCATGCTAAAGGACTAGTTTGGGAGTGGTTGGTTAAAACAGAATGGAAT
GCC

Alignment

ORF - retro_mmul_1507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 84.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQYRQLLSDYGPPSLGYTQGTGNSQV-PQSKYAELLAIIEELGK-EIRPTYAGSKSAMERLKRGIIHARG
          SQY.QLLSDY.PPSLGYTQGTGNSQV.PQS..A.LLAII.ELG...IRPTY.GSKS...R.K...IHA.G
Retrocopy SQYHQLLSDYRPPSLGYTQGTGNSQV>PQSRCAKLLAIIQELGE<VIRPTYTGSKSTVKRPKQVTIHAKG

Parental  LVRECLAETERNA
          LV.E.L..TE.NA
Retrocopy LVWEWLVKTEWNA

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	50.09 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	40.06 RPM
SRP007412_cerebellum	0.00 RPM	52.69 RPM
SRP007412_heart	0.00 RPM	39.04 RPM
SRP007412_kidney	0.00 RPM	25.94 RPM
SRP007412_liver	0.00 RPM	13.81 RPM
SRP007412_testis	0.00 RPM	41.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1507 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1507 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2834
Pan troglodytes	retro_ptro_1921
Gorilla gorilla	retro_ggor_1968
Pongo abelii	retro_pabe_2198

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015147	1 retrocopy	retro_amel_19,
Choloepus hoffmanni	ENSCHOG00000010939	1 retrocopy	retro_chof_56,
Gorilla gorilla	ENSGGOG00000009567	1 retrocopy	retro_ggor_1968,
Macropus eugenii	ENSMEUG00000009438	12 retrocopies	retro_meug_1101, retro_meug_1112, retro_meug_1218, retro_meug_1366, retro_meug_1509, retro_meug_1565, retro_meug_2116, retro_meug_377, retro_meug_404, retro_meug_669, retro_meug_836, retro_meug_868,
Macaca mulatta	ENSMMUG00000000434	1 retrocopy	retro_mmul_1507 ,
Macaca mulatta	ENSMMUG00000011827	5 retrocopies	retro_mmul_1712, retro_mmul_640, retro_mmul_728, retro_mmul_730, retro_mmul_763,
Monodelphis domestica	ENSMODG00000012451	2 retrocopies	retro_mdom_1845, retro_mdom_611,
Mus musculus	ENSMUSG00000029394	1 retrocopy	retro_mmus_125,
Rattus norvegicus	ENSRNOG00000001070	3 retrocopies	retro_rnor_1717, retro_rnor_1718, retro_rnor_1753,
Sarcophilus harrisii	ENSSHAG00000015009	1 retrocopy	retro_shar_366,