RetrogeneDB ID: retro_mmul_1164

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:90251942..90252306(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C17ORF106
• Ensembl ID: ENSMMUG00000029820
• Aliases: None
• Description: None

Sequence

>retro_mmul_1164
ATGCTGCCCAAACCCGGGACCTATTCCCTCCACTGGGAGGTCAATGCAAGCCAAGTTCCTGGTGGGTCACACTGAGAACA
TTTGACAGGTTGTACCTCTATGACATGATCAGTCCAGAGTGACACTGATGGCTCAGCATGGATCTGATCGGCACCAGGTT
CTTGTCTGTACCAAGTTGGTGAAGCCCTTCCAAGCCCAGGTGTGCTCCCTGTACATCATCCTCGGGGGGCTGCAGGACCA
GCAGCACAGAGGCTCCATGTTAAAGGCACTGGTGCTGAACTGTGTGGAGGGAATGGACCTGCCCTTGTGAGAACAAACCA
AGCAGGAGCAGAGGCAGGACCAGCAGAAGAGGGAGGGCGGCCAG

Alignment

ORF - retro_mmul_1164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLPKPGTYYLPWEVSAGQFPDGG-TLRTFGRLCLYDMI-QSRVTLMAQHGSDQHQVLVCTKLVEPFHAQV
          MLPKPGTY.L.WEV.A.Q.P.G..TLRTF.RL.LYDMI.QSRVTLMAQHGSD.HQVLVCTKLV.PF.AQV
Retrocopy MLPKPGTYSLHWEVNASQVPGGS<TLRTFDRLYLYDMI<QSRVTLMAQHGSDRHQVLVCTKLVKPFQAQV

Parental  GSLYIVLGELQHQQDGGSLVKARVLTCVEGMNLPLLEQAIREQRLYQQERGGGQ
          .SLYI.LG.LQ.QQ..GS..KA.VL.CVEGM.LPL.EQ...EQR..QQ.R.GGQ
Retrocopy CSLYIILGGLQDQQHRGSMLKALVLNCVEGMDLPL*EQTKQEQRQDQQKREGGQ

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	1.23 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.98 RPM
SRP007412_cerebellum	0.00 RPM	0.84 RPM
SRP007412_heart	0.00 RPM	1.00 RPM
SRP007412_kidney	0.00 RPM	4.34 RPM
SRP007412_liver	0.00 RPM	3.88 RPM
SRP007412_testis	0.00 RPM	7.09 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1164 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1164 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2810
Pongo abelii	retro_pabe_3425
Callithrix jacchus	retro_cjac_582

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013878	5 retrocopies	retro_cjac_3524, retro_cjac_3525, retro_cjac_3554, retro_cjac_3890, retro_cjac_582,
Gorilla gorilla	ENSGGOG00000013858	1 retrocopy	retro_ggor_2810,
Macaca mulatta	ENSMMUG00000029820	1 retrocopy	retro_mmul_1164 ,
Nomascus leucogenys	ENSNLEG00000001980	1 retrocopy	retro_nleu_1795,
Pongo abelii	ENSPPYG00000008646	1 retrocopy	retro_pabe_3425,