RetrogeneDB ID: retro_mmus_3058

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:95912771..95913386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fxn
• Ensembl ID: ENSMUSG00000059363
• Aliases: Fxn, FA, FARR, Frda, X25
• Description: frataxin [Source:MGI Symbol;Acc:MGI:1096879]

Sequence

>retro_mmus_3058
GCGTTCAGAGGTCGCGCAGCCGCGGGCTTGGTGCCCCGGACGGCGTCCCGGGCCCTCTGCCTGGGTCGGGAACCCGTGCT
GGAGTGAACTGATTTTAACCTGCGGCCGCCGAGGCCTACATGTCACAGCCAACGCCGGCGCCACCCGCCATGCCCGTTTG
AACCTCCACTACCTCCAGATTCTGAACATCAAAAAGCAGAGCATCTGCGTGGTGCATTTGAGGAACTTGGGGACATTGGA
CAACCCAAGCTCTCTAGATGAGACAGCATATGAAAGACTGGCGGAAGAGACCCTGGACTCCCTGGCAGAGTTCTTTGAAG
ACCTTGCAGATAAGCCCTATACCCTGGAGGACTACGATGTCTCTTTTGGGGATGGCGTGCTCACCATTAAGCTGGGTGGG
ATCTAGGGACCTACGTGATCAACAAGCAGACCGCAAACAAGCAAATCTGGTTGTCTTCTCCTTCCAGAGGCCCCAAGCGC
TATGACTGGACCGGGAAGAACTGGGTGTACTCTCATGACGGCGTGTCTCTGCATGAGCTGCTGGCCAGGGAGCTGACTAA
AGCTTTAAACACCAAACTGGACTTGTCTTCATTGGCCTATTCTGGAAAAGGCACT

Alignment

ORF - retro_mmus_3058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AFGGRAAVGLLPRTASRA-SAWVGNPRWREPIVTCGRRGLHVTVNAGATRHAHLNLHYLQILNIKKQSVC
          AF.GRAA.GL.PRTASRA.SAWVGNP.W.E.I.TCGRRGLHVT.NAGATRHA.LNLHYLQILNIKKQS.C
Retrocopy AFRGRAAAGLVPRTASRA>SAWVGNPCWSELILTCGRRGLHVTANAGATRHARLNLHYLQILNIKKQSIC

Parental  VVHLRNLGTLDNPSSLDETAYERLAEETLDSLAEFFEDLADKPYTLEDYDVSFGDGVLTIKLGG-DLGTY
          VVHLRNLGTLDNPSSLDETAYERLAEETLDSLAEFFEDLADKPYTLEDYDVSFGDGVLTIKLGG.DLGTY
Retrocopy VVHLRNLGTLDNPSSLDETAYERLAEETLDSLAEFFEDLADKPYTLEDYDVSFGDGVLTIKLGG<DLGTY

Parental  VINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLARELTKALNTKLDLSSLAYSGKGT
          VINKQT.NKQIWLSSPS.GPKRYDWTGKNWVYSHDGVSLHELLARELTKALNTKLDLSSLAYSGKGT
Retrocopy VINKQTANKQIWLSSPSRGPKRYDWTGKNWVYSHDGVSLHELLARELTKALNTKLDLSSLAYSGKGT

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	3.34 RPM
SRP007412_cerebellum	0.00 RPM	3.91 RPM
SRP007412_heart	0.03 RPM	12.79 RPM
SRP007412_kidney	0.00 RPM	7.93 RPM
SRP007412_liver	0.03 RPM	5.65 RPM
SRP007412_testis	0.05 RPM	1.97 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3058 was not detected

EST

No EST(s) were mapped for retro_mmus_3058 retrocopy.

TSS

No TSS is located nearby retro_mmus_3058 retrocopy 5' end.

Lab

retro_mmus_3058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3058 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,