RetrogeneDB ID: retro_mmul_2038

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:127046654..127047006(+)
• 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_2038
GTCCATTTGATGAATTTGATGAAAATGTTAACTTGGTGTGGCCAAAGCTCTCTAGGTAAGGCCACCTATAAACGACTGGC
AGAGATGACAAATGTGTTGGCAGATTGGCTATTTGTTTTTTGAAAGCTTAAAAACAAATCGTACACAGTTGAGATTTAAG
ATGTCTAAGTTTGGTAGTAGTATTTTAGTAACTAAACTGTGTGGAGATAGAGGAGCCTACAGGATGAACAAGCAAACCCC
AAATAATCAAATCTGGTTCTCTCTTCCATCTAATGGACCCAAGAATTATGATTGGAATGGGAACAACTGGGTCTATTCCC
ACAACAACTGTGTACCTCTCCACGAACTGCTG

Alignment

ORF - retro_mmul_2038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.46 %
• Parental protein coverage: 54.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VYLMNLRKSGTLGHPGSLDDTTYERLAEETLDSLAEF---FEDLADKPYTFEDYDV-SFGSGVLTVKLGG
          V.LMNL.K..T.....SL...TY.RLA.E....LA.....F..L..K.YT.E..DV..FGS..L..KL.G
Retrocopy VHLMNLMKMLTWCGQSSLGKATYKRLA-EMTNVLADWLFVF*KLKNKSYTVEI*DV>KFGSSILVTKLCG

Parental  DLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDG-VSLHELL
          D.G.Y..NKQTPN.QIW.S.PS.GPK.YDW.G.NWVYSH...V.LHELL
Retrocopy DRGAYRMNKQTPNNQIWFSLPSNGPKNYDWNGNNWVYSHNNCVPLHELL

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	0.00 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_2038 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2038 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2203
Equus caballus	retro_ecab_311

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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,