RetrogeneDB ID: retro_mmul_2491

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:41775133..41775784(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9854
• Ensembl ID: ENSMMUG00000031284
• Aliases: None
• Description: None

Sequence

>retro_mmul_2491
ATTGAAAGTATCCAGCTGATGATAGACAGTGAAACTGGTCGATCCAAGGGATATGGATTTATTACATTTTCTGATTCAGA
ATGTGCCAAAAAGGCTTTGTAACAATTTAATGGATTCGAACTAGCAGGAAGGCCAATGAAAGTTGGTCACGTTACTGAAC
GTGCTGATGCTTCGAGTACTAGTTCATTTTTGGACAGTGACGAACTGGAAAGGACTAGAATTGATTTGGGAACAACTGGT
CGTCTTCAGTTAATGGCAAGACTTGCAGAGAATACAGGTTTGCAGATTCCACCAGCTGCACAGCAAGCTCTACAAATGAG
TGGCTCTTTGGCATTTGGTGCTGTGGCAGAATTCTCTTTTGTTATAGATTTGCAAACAAGACTTTCCCAGCAGACTGAAG
CTTCAGCTTTAGCTGCAGCTGCCTCTGTTCAGCCACTTGCAACACAGTGTTTCCAACTCTCTAACATGTTTAACCCTCAA
ACAGAAGAAGTTGTATGGGATACAGAGATTAAAGACGATGTGATTGAAGAATGTAATAAACATGGAGGAGTTATTCATAT
TTATGTGGACAAAAATTCAGCTCAGGGCAATGTGTGTGTGAAGTGCCCATCAATTGCTACAACATTGCTGTCAATGCATT
GCATGGTAGGT

Alignment

ORF - retro_mmul_2491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.83 %
• Parental protein coverage: 85.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDASSASSFLDSDELE
          IESIQLM.DSETGRSKGYGFITFSDSECAKKAL.Q.NGFELAGRPMKVGHVTER.DASS.SSFLDSDELE
Retrocopy IESIQLMIDSETGRSKGYGFITFSDSECAKKAL*QFNGFELAGRPMKVGHVTERADASSTSSFLDSDELE

Parental  RTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAA
          RT.IDLGTTGRLQLMARLAE.TGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAA
Retrocopy RTRIDLGTTGRLQLMARLAENTGLQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAA

Parental  ASVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAI
          ASVQPLATQCFQLSNMFNPQTEE.V.WDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNV.VKCPSIA...
Retrocopy ASVQPLATQCFQLSNMFNPQTEEVV-WDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVCVKCPSIATTL

Parental  AAVNALHG
          .......G
Retrocopy LSMHCMVG

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	1.01 RPM	34.18 RPM
SRP007412_brain_prefrontal_cortex	0.56 RPM	32.13 RPM
SRP007412_cerebellum	2.00 RPM	59.02 RPM
SRP007412_heart	0.65 RPM	22.26 RPM
SRP007412_kidney	0.70 RPM	51.76 RPM
SRP007412_liver	0.59 RPM	29.93 RPM
SRP007412_testis	0.57 RPM	22.43 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2491 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2491 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017535	1 retrocopy	retro_cjac_2199,
Homo sapiens	ENSG00000131051	1 retrocopy	retro_hsap_4679,
Gorilla gorilla	ENSGGOG00000003950	1 retrocopy	retro_ggor_2902,
Myotis lucifugus	ENSMLUG00000003000	1 retrocopy	retro_mluc_1152,
Macaca mulatta	ENSMMUG00000031284	1 retrocopy	retro_mmul_2491 ,
Mus musculus	ENSMUSG00000027620	3 retrocopies	retro_mmus_1512, retro_mmus_2792, retro_mmus_2793,
Nomascus leucogenys	ENSNLEG00000010350	1 retrocopy	retro_nleu_2170,
Otolemur garnettii	ENSOGAG00000011227	1 retrocopy	retro_ogar_267,
Ochotona princeps	ENSOPRG00000002183	2 retrocopies	retro_opri_55, retro_opri_913,
Pongo abelii	ENSPPYG00000010963	1 retrocopy	retro_pabe_3634,