RetrogeneDB ID: retro_mmul_826

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:90026879..90027359(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXN
• Ensembl ID: ENSMMUG00000000357
• Aliases: None
• Description: frataxin, mitochondrial [Source:RefSeq peptide;Acc:NP_001247670]

Sequence

>retro_mmul_826
ATGTGAACTCTCAGGCGCCATGCAGTTGCCGGCCTCCTGTCGTCCCCCAGCCCGGCCCAGGCCCAGACCCTCACCCGGGC
CCCGCGGCCGGCAGAGTTGGCCCCGCTCTGAGGCCTCCAGGGCCTGCCCCCTGACATGGATGCAACCTGCACACCCCACC
ACGCCAGTTCGAACCTCCATGGCCTCAACCAGATTTGGAATGTCAAAAAGCAGAGTGCCTATTTGATGAATTTGAGGAAA
TCGGGAACTTTGGGCCACTCAGGCTCTCTAGATGACACCACCTATGAAAGACTAGCAGAGGAAACACTGGACTCTTTAGA
AGAGTTTTTTGAAGACCTTGCAGACAAGCCATACACCTTTGAGGACTATGATGTTTCCTTTGGGAGTGGTGTCTTAACAG
TTAAACTGGGTGGAGATCTAGGAACCTACGTGATCAACAAGCAGACGCCAAACAAGCAAATCTGGTTATCTTCTCCATCC

Alignment

ORF - retro_mmul_826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.0 %
• Parental protein coverage: 76.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWTFGRRAVAGLLASPSPAQAQTLTRAPRLAELAQLCSRRGLRTGINATCTTHHTSSNLRGLNQIRNVKR
          M.T..R.AVAGLL.SPSPAQAQTLTRAPR.AELA.L....GL.....ATCT.HH.SSNL.GLNQI.NVK.
Retrocopy M*TLRRHAVAGLLSSPSPAQAQTLTRAPRPAELAPL*GLQGLPPDMDATCTPHHASSNLHGLNQIWNVKK

Parental  QSVYLMNLRKSGTLGHPGSLDDTTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDL
          QS.YLMNLRKSGTLGH.GSLDDTTYERLAEETLDSL.EFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDL
Retrocopy QSAYLMNLRKSGTLGHSGSLDDTTYERLAEETLDSLEEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDL

Parental  GTYVINKQTPNKQIWLSSPS
          GTYVINKQTPNKQIWLSSPS
Retrocopy GTYVINKQTPNKQIWLSSPS

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	4.48 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.62 RPM
SRP007412_cerebellum	0.00 RPM	4.00 RPM
SRP007412_heart	0.12 RPM	9.83 RPM
SRP007412_kidney	0.00 RPM	7.28 RPM
SRP007412_liver	0.00 RPM	4.79 RPM
SRP007412_testis	0.00 RPM	3.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_826 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_826 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_826 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006915	1 retrocopy	retro_amel_1496,
Choloepus hoffmanni	ENSCHOG00000005107	2 retrocopies	retro_chof_349, retro_chof_94,
Callithrix jacchus	ENSCJAG00000001695	4 retrocopies	retro_cjac_1562, retro_cjac_1927, retro_cjac_3939, retro_cjac_813,
Dasypus novemcinctus	ENSDNOG00000024066	3 retrocopies	retro_dnov_2204, retro_dnov_2317, retro_dnov_307,
Equus caballus	ENSECAG00000019174	1 retrocopy	retro_ecab_311,
Homo sapiens	ENSG00000165060	2 retrocopies	retro_hsap_1447, retro_hsap_4311,
Gorilla gorilla	ENSGGOG00000007636	3 retrocopies	retro_ggor_1112, retro_ggor_2203, retro_ggor_2881,
Macaca mulatta	ENSMMUG00000000357	2 retrocopies	retro_mmul_2038, retro_mmul_826 ,
Mustela putorius furo	ENSMPUG00000009619	2 retrocopies	retro_mputfur_501, retro_mputfur_803,
Mus musculus	ENSMUSG00000059363	2 retrocopies	retro_mmus_1571, retro_mmus_3058,
Otolemur garnettii	ENSOGAG00000031105	2 retrocopies	retro_ogar_1865, retro_ogar_476,
Rattus norvegicus	ENSRNOG00000015213	1 retrocopy	retro_rnor_2276,
Tursiops truncatus	ENSTTRG00000010336	4 retrocopies	retro_ttru_1281, retro_ttru_175, retro_ttru_546, retro_ttru_831,