RetrogeneDB ID: retro_mmul_2113

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:154388567..154389472(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2958
• Ensembl ID: ENSMMUG00000003111
• Aliases: None
• Description: None

Sequence

>retro_mmul_2113
ATGGTGGACTACAGCATGTGGGACCACATAGAGGTATCTAATGATGAAGACGAGGCGCACCCCAACATCGACAGGGCCAG
CCTCTTCCACTGGCAGCACCAGGCCCGGGGGCAGCGCATGGAGCAGTTCCAGAAAGAGAAGGAGGAACTGGACAGGGTCT
GCCATGAGTGCAAGCGCAAGGTGGCCGAGTGCCAGAGGAAGCTGAAAGAGCTGGAGGTGGCCGAGGGCCGCAAGGCAGAG
CTGGGGCGGCTGCAGGCCAAGGCGCAGCAGCTGCGCAAGGAGGATCGGGGCTGGGAGCAGAAGCTGGAGGAAATGCACAA
GAAGGAGAAGAGCATGCCCTGGAATGTGGACACACTCTGAAAAGACGGTTTCAGCAAGAGCATGGTCAACACCAAGCCCG
AGAAAGTGGAGGAGGACTCAGAGGAGGTGAGGGAGCAGAAACACAAGACCTTCGTAGAAAAGTATGAGAAACAGACCAAG
CACTTCGGCATGCTCGTCACTGGGATGACAGCCAAGAGTACCTGTCAGACAACGTCCACCTGGTGTGCGAGGAGACAGCC
AATTACTTGGTCATCTGATGCATTGATCTAGAGGTGGAGGAGAAATGTGCACTCATGGAGCAGGCAGTCCCCAAGACAAT
CGTCATGCAGTTTATCCTGGAGCTGGCCAAGAGCCTGAAGGTGGACCCCCAGGCCTGCTTCCAGCAGTTCTTCACTAAGA
CTAAGACAGCCGATCGCCAGTACATGGTGGGCTTCGACGACGAACTGGAAGCCTTCAAGGAGCATGTGCGGGTCCGTACC
AAGCTGCACATCGAGAAGGCCATGAAGGAGTACAAGGAGGAGGAGCGCGAGAAGCGGCTCGGCCCTGGCGGCCTGGACCC
CGTCGAGGTCTACGAGTCCCTCCCC

Alignment

ORF - retro_mmul_2113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.46 %
• Parental protein coverage: 79.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVDYSVWDHIEVSDDEDETHPNIDTASLFRWRHQARVERMEQFQKEKEELDRGCRECKRKVAECQRKLKE
          MVDYS.WDHIEVS.DEDE.HPNID.ASLF.W.HQAR..RMEQFQKEKEELDR.C.ECKRKVAECQRKLKE
Retrocopy MVDYSMWDHIEVSNDEDEAHPNIDRASLFHWQHQARGQRMEQFQKEKEELDRVCHECKRKVAECQRKLKE

Parental  LEVAEGGKAELERLQAEAQQLRKEERSWEQKLEEMRKKEKSMPWNVDTLSKDGFSKSMVNTKPEKTEEDS
          LEVAEG.KAEL.RLQA.AQQLRKE.R.WEQKLEEM.KKEKSMPWNVDTL.KDGFSKSMVNTKPEK.EEDS
Retrocopy LEVAEGRKAELGRLQAKAQQLRKEDRGWEQKLEEMHKKEKSMPWNVDTL*KDGFSKSMVNTKPEKVEEDS

Parental  EEVREQKHKTFVEKYEKQIKHFGML-RRWDDSQKYLSDNVHLVCEETANYLVIWCIDLEVEEKCALMEQV
          EEVREQKHKTFVEKYEKQ.KHFGML.R.WDDSQ.YLSDNVHLVCEETANYLVI.CIDLEVEEKCALMEQ.
Retrocopy EEVREQKHKTFVEKYEKQTKHFGML<RHWDDSQEYLSDNVHLVCEETANYLVI*CIDLEVEEKCALMEQA

Parental  AHQTIVMQFILELAKSLKVDPRACFRQFFTKIKTADRQYMEGFNDELEAFKERVRGRAKLRIEKAMKEYE
          ...TIVMQFILELAKSLKVDP.ACF.QFFTK.KTADRQYM.GF.DELEAFKE.VR.R.KL.IEKAMKEY.
Retrocopy VPKTIVMQFILELAKSLKVDPQACFQQFFTKTKTADRQYMVGFDDELEAFKEHVRVRTKLHIEKAMKEYK

Parental  EEERKKRLGPGGLDPVEVYESLP
          EEER.KRLGPGGLDPVEVYESLP
Retrocopy EEEREKRLGPGGLDPVEVYESLP

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	73.95 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	119.07 RPM
SRP007412_cerebellum	0.00 RPM	74.71 RPM
SRP007412_heart	0.00 RPM	117.18 RPM
SRP007412_kidney	0.00 RPM	61.03 RPM
SRP007412_liver	0.00 RPM	90.05 RPM
SRP007412_testis	0.41 RPM	128.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2113 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2113 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2113 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3396
Pongo abelii	retro_pabe_2790

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105401	1 retrocopy	retro_hsap_3396,
Gorilla gorilla	ENSGGOG00000008098	1 retrocopy	retro_ggor_2299,
Macropus eugenii	ENSMEUG00000002278	1 retrocopy	retro_meug_1373,
Macaca mulatta	ENSMMUG00000003111	1 retrocopy	retro_mmul_2113 ,
Pongo abelii	ENSPPYG00000009551	1 retrocopy	retro_pabe_2790,
Ictidomys tridecemlineatus	ENSSTOG00000015962	1 retrocopy	retro_itri_328,