RetrogeneDB ID: retro_mmul_1715

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:118401565..118402344(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL4
• Ensembl ID: ENSMMUG00000023067
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase-like 4 [Source:RefSeq peptide;Acc:NP_001245084]

Sequence

>retro_mmul_1715
GCCTGCTTTAATTTCTTGAGATTGTACAAAATAAAATATTACAATTATTGCCTTATTCACAGTGTACAAAGGGATTTTAT
CATACAAACTGTTGATCCTATAGGGACTGGTCATGGAGGAGAGTCTATTTTTGGCCAATTGTATGGTGATCAAGCGAGCT
TTTTTGAGACAGAAAACGTCCCAAGAGTTAAACACAAGAAGAAAGGCACAATGTCCTTGGTGAATAATGGCAGTGATCAA
CAGGGATCTCAGTTTCTTATCACTACAGGAGAAAATCTAGATTACCTTGATGGTACCATACAGTATTTGGTGAGGTGACA
GAAGGCATTGACATAATTAAGAAAATTAATGAGACCTTTGTTGACAAGGACTTTGTACCATATCAGGATATCAGGATAAA
TTATACAGTGATTTTAGATGATCCGTTTTGATGGCACTCCTCATTTATTAATCCCTGATCTATCACCAGAACCTACAAGT
GAACAATTAAAGAGTGGGTAGAATTGATGCAGATGAAGAAATTGATCATTTCAAAGGAAGGTCAGCTGAAGAAGTAGAAG
AACTAAAGGCAGAAAAAGAAGCTAAAACTCAGGCTTTACTTTTAGAATGGTAGGAGACCTACCTGATGCAGATATTAAAC
CTCCAGAAAAATCTGCTGTGTTTGTAAATTGAATCCAGTGACTACAGATGAGGATCTGGATATAATACTCTCTAGATTTG
GGCCAATAAGAAGTTGTGAAGTTATCTGGGACTGGAAGACAGGAGAAACCCTCTGTTAT

Alignment

ORF - retro_mmul_1715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 52.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTGRGGESIFGQLYGDQASFFEAEKVPRIKHKKKGT
          AC.NFL.L.KIKYYNYCLIH.VQRDFIIQT.DP.GTG.GGESIFGQLYGDQASFFE.E.VPR.KHKKKGT
Retrocopy ACFNFLRLYKIKYYNYCLIHSVQRDFIIQTVDPIGTGHGGESIFGQLYGDQASFFETENVPRVKHKKKGT

Parental  VSMVNNGSDQHGSQFLITTGENLDYLDGV-HTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVIL
          .S.VNNGSDQ.GSQFLITTGENLDYLDG..HTVFGEVTEG.DIIKKINETFVDKDFVPYQDIRIN.TVIL
Retrocopy MSLVNNGSDQQGSQFLITTGENLDYLDGT<HTVFGEVTEGIDIIKKINETFVDKDFVPYQDIRINYTVIL

Parental  DDP-FDDPPDLLIPDRSPEPTREQLDS-GRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLE-MVGD
          DDP.FD..P.LLIPD.SPEPT.EQL.S.GRI.ADEEID.FKGRSAEEVEE.KAEKEAKTQA.LLE.MVGD
Retrocopy DDP>FDGTPHLLIPDLSPEPTSEQLKS>GRIDADEEIDHFKGRSAEEVEELKAEKEAKTQALLLE<MVGD

Parental  LPDADIKPPE-NVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCY
          LPDADIKPPE.....VCKLNPVTTDEDL.II.SRFGPIRSCEVI.DWKTGE.LCY
Retrocopy LPDADIKPPE<KICCVCKLNPVTTDEDLDIILSRFGPIRSCEVIWDWKTGETLCY

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	7.51 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	2.78 RPM
SRP007412_cerebellum	0.45 RPM	7.68 RPM
SRP007412_heart	0.00 RPM	5.83 RPM
SRP007412_kidney	0.12 RPM	6.46 RPM
SRP007412_liver	0.00 RPM	1.58 RPM
SRP007412_testis	0.04 RPM	7.73 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1715 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1715 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019613	1 retrocopy	retro_cjac_2963,
Macaca mulatta	ENSMMUG00000013129	1 retrocopy	retro_mmul_1124,
Macaca mulatta	ENSMMUG00000023067	1 retrocopy	retro_mmul_1715 ,
Nomascus leucogenys	ENSNLEG00000015316	1 retrocopy	retro_nleu_173,
Oryctolagus cuniculus	ENSOCUG00000007696	2 retrocopies	retro_ocun_661, retro_ocun_892,
Taeniopygia guttata	ENSTGUG00000010655	1 retrocopy	retro_tgut_16,