RetrogeneDB ID: retro_mmul_2100

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:106145299..106145865(-)
• Located in intron of: ENSMMUG00000003316

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000021984
• Aliases: None
• Description: None

Sequence

>retro_mmul_2100
ATGACTGATAAAGCAGAGAAGGTTGCTGTAGAACCTGAAAACGTGTTTAAATGTCATAGGGAATCGAGAGTCCTTCATCT
CAGAAAAGGCAGAAGATGGCCCTGTTGTTAAGGAAACAAAGAGCAGGAGACAGCCTTATTGGAGGTTCTACCATGTCCAA
GGAAAAGAAGCTTATGGCAGGAGATGGTATTCCACCAAGCCAATTGGATTCTTGGTTTGATGATTTCAGTGGTTTCAGCA
AAGATGGGCTGATGCAGAAACCTGGTAGAAATGCACCTGTTAGAGGAATCATTACCAGGAATTTCTCTGGAGATGACCTA
AAAGTCACAGAAATACTCCCTTTTCCAAAAAGCCAAGAAGAAATTAATGTTGATATAAAATGTCAATTAGTGAAGGAAAT
TCGACACTTTGGACGAAAATATGAAAAACTCTTCAAATTGCTTGAAGGACTGCAAGGACCTATGGAAGTCAAGAAATGAT
TTTTTGAATCCATCATCAAGGAAGCCACAAGATTTATGAGGCGAGACTTAATTCAGCACCTTGAGAAGAAACTGGAACAA
ATGATT

Alignment

ORF - retro_mmul_2100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDKTEKVAVDPETVFKRPREC-DSPSYQKRQKMALLARKQGAGDSLTAGSAMSKEKKHKTGHGVLPSQL
          MTDK.EKVAV.PE.VFK..RE...SPS.QKRQKMALL.RKQ.AGDSL..GS.MSKEKK...G.G..PSQL
Retrocopy MTDKAEKVAVEPENVFKCHRES<ESPSSQKRQKMALLLRKQRAGDSLIGGSTMSKEKKLMAGDGIPPSQL

Parental  DSQIDDFADFSKDGLMQKPGSNAPVGGIITSNFSGDDLKCREIIPFPKSQEEINADIKCQLVKEIRSIGR
          DS..DDF..FSKDGLMQKPG.NAPV.GIIT.NFSGDDLK..EI.PFPKSQEEIN.DIKCQLVKEIR..GR
Retrocopy DSWFDDFSGFSKDGLMQKPGRNAPVRGIITRNFSGDDLKVTEILPFPKSQEEINVDIKCQLVKEIRHFGR

Parental  KYEKIFKLLEGVQGPIEVKKLFFESIIKEAARYISRDFVQLLEKKLEHMI
          KYEK.FKLLEG.QGP.EVKK.FFESIIKEA.R...RD..Q.LEKKLE.MI
Retrocopy KYEKLFKLLEGLQGPMEVKK*FFESIIKEATRFMRRDLIQHLEKKLEQMI

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.13 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.12 RPM	0.00 RPM
SRP007412_liver	0.04 RPM	0.00 RPM
SRP007412_testis	0.04 RPM	1.62 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2100 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2100 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3362
Pan troglodytes	retro_ptro_2285
Pongo abelii	retro_pabe_2766
Callithrix jacchus	retro_cjac_1827

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014436	2 retrocopies	retro_cfam_441, retro_cfam_444,
Callithrix jacchus	ENSCJAG00000004135	1 retrocopy	retro_cjac_1827,
Dipodomys ordii	ENSDORG00000008443	1 retrocopy	retro_dord_354,
Homo sapiens	ENSG00000242284	1 retrocopy	retro_hsap_3362,
Macaca mulatta	ENSMMUG00000021984	1 retrocopy	retro_mmul_2100 ,
Nomascus leucogenys	ENSNLEG00000002303	1 retrocopy	retro_nleu_961,
Pongo abelii	ENSPPYG00000020755	1 retrocopy	retro_pabe_2766,
Pan troglodytes	ENSPTRG00000041730	1 retrocopy	retro_ptro_2285,