RetrogeneDB ID: retro_mmul_1035

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:81862044..81862573(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDP1
• Ensembl ID: ENSMMUG00000012476
• Aliases: None
• Description: None

Sequence

>retro_mmul_1035
GAGAACAGACTATCAGAGAACCATAGTTTCAAGAATAAGAAAGCTGCTCTGTGGGCTTTACAGAGGAAGGAAAGATTGGG
ACAGCAGCTGGCACAAACTGATGGAACATTATCCCCTCTGGAGTTTCAGCATGAAGCCGTTGAGAATGCCACTACCAATG
CAAACATGTTTCGTACCTTGTAGTTAGCTGCCCGAGGCATAAAGAAGGCCTCCCAGGACCTGGACACTGGCAAGGTAGAT
GAACAGATGGATGACATCACAGACTAGCAGGAGGTGGCCCAGCAGATCTCAGATGCATTTCTTGACCTGTGGGTTTTGGA
GATGTGGGTGATTGTGAACTGTTGGAGGAACTAGAGAAGCTGGAGGAAGAATTGACCCAACAATTGTTAAATATGGGGCA
ACAAGGAGGAAGTGAACCCCAGTCAAATGGCTAGCATATCCACTACACTATCTGCCTTCCTGGGAGGGTCAGCTCCCGCA
AAGCAGATGAAGACAAAGAAGCACTAAAGCAGTGGCTGTGTGGGAATCC

Alignment

ORF - retro_mmul_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.91 %
• Parental protein coverage: 79.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ELQTAKKYGTKNKRAALQALRRKKRFEQQLAQTDGTLSTLEFQREAIENATTNAEVLRTMELAAQGMKKA
          E.........KNK.AAL.AL.RK.R..QQLAQTDGTLS.LEFQ.EA.ENATTNA...RT..LAA.G.KKA
Retrocopy ENRLSENHSFKNKKAALWALQRKERLGQQLAQTDGTLSPLEFQHEAVENATTNANMFRTL*LAARGIKKA

Parental  YQDMDIDKVDELMTDITEQQEVAQQISDA-ISRPMGFGDDVDEDELLEELELLEQEELAQELLSV-GDKE
          .QD.D..KVDE.M.DIT..QEVAQQISDA.IS.P.GFG.DV...ELLEELE.LE.EEL.Q.LL...G.KE
Retrocopy SQDLDTGKVDEQMDDITD*QEVAQQISDA<IS*PVGFG-DVGDCELLEELEKLE-EELTQQLLNM>GNKE

Parental  EEPPVKLPSVPST-HLPA--EPAPKADEDEEALKQLAEWVS
          E..P....S...T..LP......P.........K..A.W.S
Retrocopy EVNPSQMASISTT>YLPSWEGQLPQSR*RQRSTKAVAVWES

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	12.55 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	23.09 RPM
SRP007412_cerebellum	0.00 RPM	21.96 RPM
SRP007412_heart	0.00 RPM	17.43 RPM
SRP007412_kidney	0.00 RPM	19.95 RPM
SRP007412_liver	0.00 RPM	10.29 RPM
SRP007412_testis	0.00 RPM	14.14 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1035 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1035 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2284
Gorilla gorilla	retro_ggor_1697
Pongo abelii	retro_pabe_1937

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000254505	1 retrocopy	retro_hsap_2284,
Gorilla gorilla	ENSGGOG00000016091	1 retrocopy	retro_ggor_1697,
Microcebus murinus	ENSMICG00000001732	1 retrocopy	retro_mmur_1101,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178,
Macaca mulatta	ENSMMUG00000012476	2 retrocopies	retro_mmul_1035 , retro_mmul_1694,
Pongo abelii	ENSPPYG00000005691	1 retrocopy	retro_pabe_1937,
Sorex araneus	ENSSARG00000008328	1 retrocopy	retro_sara_530,