RetrogeneDB ID: retro_mmul_1817

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:7425318..7425956(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000008606
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.2453
• Ensembl ID: ENSMMUG00000016077
• Aliases: None
• Description: isocitrate dehydrogenase [Source:RefSeq peptide;Acc:NP_001252708]

Sequence

>retro_mmul_1817
TCTAAGGGTTGGCCTTTGTATCTGAGCACTAAAACACTATTTTGAAGAAATATGATGAACGTTTTAAAGACATCTTTGAG
GAGATACATGACAAGCAGTACAAGTCCCAATTTGAAGCCCAAAAGATCTTGTATGAGCATAGGCTCATCGATGACATGGT
GGTCCAAGCTATGAAATCAGAAGGAGGCTTCATCTGGGCCTCTAAAAAGTATACTGGTGACGTGCAGTCAGACTCTGTGG
CTCAAGGGTATGTCTCTCTTGGCATGATGACCAGTGTGCTGGTGTGTCCGCAAGGTAAGACAGTAGAAGCAGTGGCTGCC
CACTGGACTGTAACCTGTCACTACCGCATGTCCCAGAAAGGCCAGGAGACGTCCATCAATCCCATTGCTTCTATTTTTGC
CTGTACCAGAGGGTTGGCCCTCAGAGCAAAGATTGATAACGATAAAGAGCTTGGCTTCTTTGCAAATGCTTTGGAAGAAG
TCTGTATTGAGACAACTGAGGCTGGTTTCATGACCGAGGACTTGGCTGCTAGCATTAAAGGTTTACCCAGTGTGCAATGT
TCTGACTACTTGAATATGTTTGAGTTCATGGACAAACTTGGAGAAAACTTGAAGATCAAACTGGCTCAGGCCAAACTT

Alignment

ORF - retro_mmul_1817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.38 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKGWPLYLSTK-NTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACK
          SKGWPLYLSTK.NTILKKYD.RFKDIF.EI.DKQYKSQFEAQKI.YEHRLIDDMV.QAMKSEGGFIWA.K
Retrocopy SKGWPLYLSTK<NTILKKYDERFKDIFEEIHDKQYKSQFEAQKILYEHRLIDDMVVQAMKSEGGFIWASK

Parental  NYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGL
          .Y.GDVQSDSVAQGY.SLGMMTSVLVCP.GKTVEA.AAH.TVT.HYRM.QKGQETS.NPIASIFA.TRGL
Retrocopy KYTGDVQSDSVAQGYVSLGMMTSVLVCPQGKTVEAVAAHWTVTCHYRMSQKGQETSINPIASIFACTRGL

Parental  AHRAKLDNNKELAFFANALEEVCIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLA
          A.RAK.DN.KEL.FFANALEEVCIET.EAGFMT.DLAA.IKGLP.VQ.SDYLN.FEFMDKLGENLKIKLA
Retrocopy ALRAKIDNDKELGFFANALEEVCIETTEAGFMTEDLAASIKGLPSVQCSDYLNMFEFMDKLGENLKIKLA

Parental  QAKL
          QAKL
Retrocopy QAKL

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	21.18 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.42 RPM
SRP007412_cerebellum	0.00 RPM	14.53 RPM
SRP007412_heart	0.00 RPM	45.87 RPM
SRP007412_kidney	0.00 RPM	137.20 RPM
SRP007412_liver	0.00 RPM	233.54 RPM
SRP007412_testis	0.04 RPM	42.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1817 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1817 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1817 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2935

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020527	1 retrocopy	retro_btau_1235,
Choloepus hoffmanni	ENSCHOG00000004574	2 retrocopies	retro_chof_2158, retro_chof_897,
Cavia porcellus	ENSCPOG00000013587	1 retrocopy	retro_cpor_1010,
Homo sapiens	ENSG00000138413	1 retrocopy	retro_hsap_3554,
Gorilla gorilla	ENSGGOG00000012619	1 retrocopy	retro_ggor_2400,
Microcebus murinus	ENSMICG00000009797	1 retrocopy	retro_mmur_1364,
Macaca mulatta	ENSMMUG00000016077	1 retrocopy	retro_mmul_1817 ,
Nomascus leucogenys	ENSNLEG00000007143	3 retrocopies	retro_nleu_1169, retro_nleu_2328, retro_nleu_3117,
Otolemur garnettii	ENSOGAG00000014848	4 retrocopies	retro_ogar_1488, retro_ogar_2270, retro_ogar_2925, retro_ogar_3057,
Pongo abelii	ENSPPYG00000013125	2 retrocopies	retro_pabe_2935, retro_pabe_926,
Pan troglodytes	ENSPTRG00000012865	1 retrocopy	retro_ptro_2415,
Sus scrofa	ENSSSCG00000023264	1 retrocopy	retro_sscr_549,