RetrogeneDB ID: retro_mmul_2511

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:80335749..80336362(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDK1
• Ensembl ID: ENSMMUG00000022553
• Aliases: None
• Description: None

Sequence

>retro_mmul_2511
AGTCTATCTCCTGAAAAACATATTGCAAACATAAATACAAACTACAATGTAGACAAAGTTATTAAATATGGCTATGAAAG
TGCTACACATCTGTGTGATTTGTATTATATTAATTCTTCCAAATTCAAACATGCAGAAGTAAATATAAAGCCATGACGAC
AACCAGTGTAAGTGGGTGATGTACCATCGTATCTCTTTCACCTGGTGTTTGAATTTTTCAAGAATGCAATGGGAACAACT
ATGGGCCATCATGTCAATGAAGTGTTTATCCCCCTATTCAAGTTTCTGTCACACTGGGTAATAAAGATTTGACTGTAAAA
TGAGTCACTGAGGAAGTAGTGTTCTTTTGAGGAAAACTGACAGACTCTTCATCTACATGTGTTCAAGTGCACCACATCCT
GGTGCTGAGATTTTCTGAGCAGTGTTTCTGGCTAGGTTTGGTTACAGATTGCCCATGTCATGTCTTTATACACAATACTA
CCAAGGAGATCTAATGCTATATTCCCTGGAGGGTTATGAAACAGACACAGCTATCTACATTAAAGCACTGCCAACAGAAT
CAATAGAAAGACTCCAAGTGTATAATAAAACTGCCTGGAAATATTACAACACT

Alignment

ORF - retro_mmul_2511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.11 %
• Parental protein coverage: 52.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPSHRKHIGSINPNCNVVEVIKDGYENARRLCDLYYINSPELELGELNAKSPGQPIQVVYVPSHLYHMVF
          S.S..KHI..IN.N.NV..VIK.GYE.A..LCDLYYINS......E.N.K...QP..V..VPS.L.H.VF
Retrocopy SLSPEKHIANINTNYNVDKVIKYGYESATHLCDLYYINSSKFKHAEVNIKP*RQPV*VGDVPSYLFHLVF

Parental  ELFKNAMRATMEHHANR-GVYPPIQVHVTLGNEDLTV-KMSDRGGGVPLRKIDRLFNYMYSTAPRPRVET
          E.FKNAM..TM.HH.N...VYPPIQV.VTLGN.DLTV.KMS..G..V.LRK.DRLF.YM.S.AP.P..E.
Retrocopy EFFKNAMGTTMGHHVNE<SVYPPIQVSVTLGNKDLTV<KMSH*GSSVLLRKTDRLFIYMCSSAPHPGAEI

Parental  SRAVPLVLCFCQLPSTCSSCQISGIRINKILIECYLICFFFFFQALSTDSIERLPVYNKAAWKHYNT
          ..AV.L......LP..C...Q...........E.Y.........AL.T.SIERL.VYNK.AWK.YNT
Retrocopy F*AVFLARFGYRLPMSCLYTQYYQGDLMLYSLEGYETDTAIYIKALPTESIERLQVYNKTAWKYYNT

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	3.47 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.30 RPM
SRP007412_cerebellum	0.00 RPM	4.26 RPM
SRP007412_heart	0.00 RPM	8.01 RPM
SRP007412_kidney	0.00 RPM	5.40 RPM
SRP007412_liver	0.00 RPM	1.39 RPM
SRP007412_testis	0.00 RPM	24.99 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2511 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2511 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007507	1 retrocopy	retro_cjac_4090,
Cavia porcellus	ENSCPOG00000008434	1 retrocopy	retro_cpor_545,
Macaca mulatta	ENSMMUG00000022553	1 retrocopy	retro_mmul_2511 ,
Monodelphis domestica	ENSMODG00000009035	2 retrocopies	retro_mdom_107, retro_mdom_1447,
Otolemur garnettii	ENSOGAG00000014761	1 retrocopy	retro_ogar_509,