RetrogeneDB ID: retro_mmul_388

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:91931427..91932306(+)
• Located in intron of: ENSMMUG00000000665

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9535
• Ensembl ID: ENSMMUG00000011838
• Aliases: None
• Description: isocitrate dehydrogenase [Source:RefSeq peptide;Acc:NP_001247734]

Sequence

>retro_mmul_388
ATGGCTGGGCCCGGGTGGATCTCCAAGGTCTGTCTGCTGCTGGGGGTATTCCACAACCCAAAACAGGTGACTAGAGGTTT
TACTGATGTTGTTCAGCCAGTGACTTTAATTCCAGGAGATGGTATTGCCCCAGAAATTTCAGCTGCAGTTATGAAGATTT
TTGATGCTGCCTAAGCACCTATTCAGTGGGAGGAGCGGAACGTCACTGCCATTCAAGGACCTGGAGGAAAGTGGACGATC
CCTTTGGAGGCTAAAGAGTCCATGGATAAGAACAAGATGGGCTTGAAAGGCCCTTTGAAGACCCCAAAAGCAGCCGGTCA
CCCATCTATGAATTTGCCGCTGCGCAAAACATTGGAGCTTTACACAAATGTCCGGCCATGTGTCTCTATCTAAGGCTATA
AAACCCCTTACACCGATGTAAATATTGTGACCATTCGAGAGAACACAGAAGGAGAATACAGTGGAATTGAGCATGTGATC
ATTGATGAAGTTGTGCAGAGTATCAAGCTCATCACCGAGGGGGCGAGCAAGCCCATTGCTGAGTTTGCCTTTGAGTATGC
CCGGAACAACCACCGGAACAAAGTCACGGCGGTGCACAAAGCCAACATCATGCGGATGTTAGACGGGCTTTTTCTACAAA
AATGCAGGGAAGTTGTAGAAAACTGTACAGATATTAAATTTAATGAGATGTACCTTGATACAGTATGTTTGAATATGGTA
CAAGATTCTTCCCAATTTGATGTTGTTGTTATGCCAAATTTGTATGGAGACATCCTTAGTGACCTGTGGGCAGGATTGAT
CGGAGGTCTTGGTGTGATGCCAAGTGGCAACATTGGAGCCAATGGGGTTGCAATTTTTGAGTCGATTCATGGGACGGCT

Alignment

ORF - retro_mmul_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.76 %
• Parental protein coverage: 80.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGPAWISKVSRLLGAFHNPKQVTRGFTGGVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTA
          MAGP.WISKV..LLG.FHNPKQVTRGFT..VQ.VTLIPGDGI.PEISAAVMKIFDAA.APIQWEERNVTA
Retrocopy MAGPGWISKVCLLLGVFHNPKQVTRGFTDVVQPVTLIPGDGIAPEISAAVMKIFDAA*APIQWEERNVTA

Parental  IQGPGGKWMIPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDV
          IQGPGGKW.IP.EAKESMDKNKMGLKGPLKTP.AAGHPSMNL.LRKT..LY.NVRPCVSI.GYKTPYTDV
Retrocopy IQGPGGKWTIPLEAKESMDKNKMGLKGPLKTPKAAGHPSMNLPLRKTLELYTNVRPCVSI*GYKTPYTDV

Parental  NIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMSDGL
          NIVTIRENTEGEYSGIEHVI.D.VVQSIKLITEGASK.IAEFAFEYARNNHR..VTAVHKANIMRM.DGL
Retrocopy NIVTIRENTEGEYSGIEHVIIDEVVQSIKLITEGASKPIAEFAFEYARNNHRNKVTAVHKANIMRMLDGL

Parental  FLQKCREVAENCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGA
          FLQKCREV.ENC.DIKFNEMYLDTVCLNMVQD.SQFDV.VMPNLYGDILSDL.AGLIGGLGV.PSGNIGA
Retrocopy FLQKCREVVENCTDIKFNEMYLDTVCLNMVQDSSQFDVVVMPNLYGDILSDLWAGLIGGLGVMPSGNIGA

Parental  NGVAIFESVHGTA
          NGVAIFES.HGTA
Retrocopy NGVAIFESIHGTA

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	0.34 RPM	91.88 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	79.17 RPM
SRP007412_cerebellum	0.19 RPM	97.77 RPM
SRP007412_heart	0.00 RPM	81.91 RPM
SRP007412_kidney	0.00 RPM	50.00 RPM
SRP007412_liver	0.16 RPM	10.09 RPM
SRP007412_testis	0.04 RPM	27.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_388 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_388 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000009646	1 retrocopy	retro_meug_1784,
Macaca mulatta	ENSMMUG00000011838	1 retrocopy	retro_mmul_388 ,
Sorex araneus	ENSSARG00000001186	1 retrocopy	retro_sara_692,
Sarcophilus harrisii	ENSSHAG00000017922	1 retrocopy	retro_shar_410,