RetrogeneDB ID: retro_mmul_1231

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:38835755..38836859(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.869
• Ensembl ID: ENSMMUG00000007539
• Aliases: None
• Description: None

Sequence

>retro_mmul_1231
AATAACCATGGACTCCAAGCACAGCAGCAACAGCAAAAGAATCTCTCACTACATGGATACATGAGTATGGAGTTATTGCA
AGAAGATAGTGTCTCCGTTCCCAAAGGATATGTGGCAAAATCAACAGATGAAGCTTATGCAGTTGCCAAAAAATTAGGTT
CAAAAGATGTTGTGATAAAGGCCCAAGTTTTATCTGGTGGTAGAGAAAAAGGAACATTCGAAAGTGGCCTCAAAGGAGGA
GTGAAGATAGTTTTCTCTCCAGAAGAAGCAAGAGCTATTTCTTCACAAATGATTGGGGAAAAATTGTTTACCAAGCTAAC
GGGAGACAAGGGCAGAATATGCAACCAAGTATTGGTCTGTGAGCGAAAGTATCCCAGGAGAGACGACTACTTTGCAATAA
CAATGGAAAGGTCATTTCAAGGTCCTGTATTAACAGGAAGTTCACATGGTGGTGTCAACATTGAAGATGTTGCTGCCGAG
ACTCCTGAAGCAATAATTAAAGAACCTATTGATATTGAAGAAGGCATCAAAAAGGAACAAGCTCTCCAGCTTGCACAGAA
GATGGGATTTCCCCCTAATATTGTGGAATCACAGCATAATACATGGTCTAGCTTTACAGCCTTTTTCTGAAATATGATGC
AACCATGATAGAAATAAATCCAGTGGTGGAAGATTCAGATGGAGCTGTATTGTGTATGGATGCAAAGATCAATTTTGACT
CGAATTCAGCCTATCACCAAAAGAAAATCTTTGATCTACAGGACTGGACCCAGGAAGATGAAAGGGACAAAGATGCTGCT
AAGGCAAATCTCAACTGCATTGGCCTCAATGGAAATACAGGCTGCCTAGTAAATGGTGCTGGTTTGGCTGTGGCCACAAT
GGATACAATAAAACTTCATGGAGGGCCTCCAGCCAACTTCCTTGATGTTGGTGGTGATGCTACAGTCTATCGAGTAACAG
AAGCATTTAAGCTTATCACCTCCAGATAAAAAGGTACTGGCTATTCTGGTCAACAATTTTGGAGGAATCATGCACTGTGA
TGTTATTGCACAGGGTATAGTCATGGCAGTAAAAGATTTGGAAATTAAAATACCTGTTATGGTA

Alignment

ORF - retro_mmul_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.38 %
• Parental protein coverage: 80.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NNHGLQVQQQQQRNLSLHEYMSMELLQEAGVSIPKGCVAKSPDEAYAVAKKLGSKDVVIKAQVLAGGRGK
          NNHGLQ.QQQQQ.NLSLH.YMSMELLQE..VS.PKG.VAKS.DEAYAVAKKLGSKDVVIKAQVL.GGR.K
Retrocopy NNHGLQAQQQQQKNLSLHGYMSMELLQEDSVSVPKGYVAKSTDEAYAVAKKLGSKDVVIKAQVLSGGREK

Parental  GTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCERKYPRREYYFAITMERSFQ
          GTFESGLKGGVKIVFSPEEA.A.SSQMIG.KLFTK.TG.KGRICNQVLVCERKYPRR..YFAITMERSFQ
Retrocopy GTFESGLKGGVKIVFSPEEARAISSQMIGEKLFTKLTGDKGRICNQVLVCERKYPRRDDYFAITMERSFQ

Parental  GPVLIGSSQGGVNIEDVAAETPEAIITEPIDIEEGIKKEQALQLAQKMGFPPNIVES-AAENMVKLYSLF
          GPVL.GSS.GGVNIEDVAAETPEAII.EPIDIEEGIKKEQALQLAQKMGFPPNIVES..A..MV.LYSLF
Retrocopy GPVLTGSSHGGVNIEDVAAETPEAIIKEPIDIEEGIKKEQALQLAQKMGFPPNIVES<TA*YMV*LYSLF

Parental  LKYDATMIEINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERDKDAAQANLNYIGLDGN
          LKYDATMIEINP.VEDSDGAVLCMDAKINFDSNSAY.QKKIFDLQDWTQEDERDKDAA.ANLN.IGL.GN
Retrocopy LKYDATMIEINPVVEDSDGAVLCMDAKINFDSNSAYHQKKIFDLQDWTQEDERDKDAAKANLNCIGLNGN

Parental  IGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVHQVTEAFKLITS-DKKVLAILVNIFGGIMRCDV
          .GCLVNGAGLA.ATMD.IKLHGG.PANFLDVGG.ATV..VTEAFKLITS.DKKVLAILVN.FGGIM.CDV
Retrocopy TGCLVNGAGLAVATMDTIKLHGGPPANFLDVGGDATVYRVTEAFKLITS>DKKVLAILVNNFGGIMHCDV

Parental  IAQGIVTALKDLEIKIPVVV
          IAQGIV.A.KDLEIKIPV.V
Retrocopy IAQGIVMAVKDLEIKIPVMV

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	2.58 RPM	73.06 RPM
SRP007412_brain_prefrontal_cortex	2.14 RPM	50.61 RPM
SRP007412_cerebellum	1.55 RPM	45.33 RPM
SRP007412_heart	3.89 RPM	68.07 RPM
SRP007412_kidney	1.29 RPM	47.65 RPM
SRP007412_liver	0.32 RPM	5.78 RPM
SRP007412_testis	0.57 RPM	20.43 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1231 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1231 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1231 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231 ,
Macaca mulatta	ENSMMUG00000009693	2 retrocopies	retro_mmul_1273, retro_mmul_1995,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,