RetrogeneDB ID: retro_rnor_2276

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:27606216..27606689(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXN
• Ensembl ID: ENSRNOG00000015213
• Aliases: None
• Description: Frataxin, mitochondrial Frataxin intermediate form Frataxin mature form [Source:UniProtKB/Swiss-Prot;Acc:D3ZYW7]

Sequence

>retro_rnor_2276
TCCATCCACAAAGTCCATGTGAACCTCTACTACCTGAGTCAGATAGTGAACAACAAAAAGCAGAGGGTCTGCATGGTGCA
TTTGAGAAACTAAGGAATGTTGAACATCAGAAGTGTTCTAGAAGAGATAACTCATCAAAGACTGCCAGAGGAGATGCTCA
ATGCCCTGATGGAGTTCTTTGAAGATCTTACAGAAAAGTCCTATACCCTGGAAGGCTATGGTGTCTCCTTCAGTGTGCCA
TGTTCATCATTAAGCTGAGTGGAGATATACAGAACTAGGTAATCAACAAGCAGAGCCCAAAGAAGCAAATCTGGCTATTT
TATCCATCTAGTAGTCCCAAGTGGTTTGACTGGACCAGGAAGAACTGGGTGTACTCCCATGACAGTGTGTCTCTGCATGG
GCTGCTGGCCTGGGATCTGACTCAAACTTTAAGTACCAAACTGAATTTGTCTTCATTGGCCTGTTTTGGAAAA

Alignment

ORF - retro_rnor_2276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.72 %
• Parental protein coverage: 75.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AIRHSHLNLHYLGQILNIKKQSVCVVHLRNSGTLGNPSSLDETAYERLAEETLDALAEFFEDLADKPYTL
          .I...H.NL.YL.QI.N.KKQ.VC.VHLRN.G.L...S.L.E....RL.EE.L.AL.EFFEDL..K.YTL
Retrocopy SIHKVHVNLYYLSQIVNNKKQRVCMVHLRN*GMLNIRSVLEEITHQRLPEEMLNALMEFFEDLTEKSYTL

Parental  KDYDVSFGVP-LCTVKYSGGRGRRIRNHRCLLLYLWFSGPCSGPKRYDWTGKNWVYSHDGVSLHELLARE
          ..Y.VSF.VP.....K.SG.......N........W...P.S.PK..DWT.KNWVYSHD.VSLH.LLA..
Retrocopy EGYGVSFSVP<MFIIKLSGDIQN*VINKQSPKKQIWLFYPSSSPKWFDWTRKNWVYSHDSVSLHGLLAWD

Parental  LTEALNTKLDLSSLAYSGK
          LT..L.TKL.LSSLA..GK
Retrocopy LTQTLSTKLNLSSLACFGK

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
SRP017611_brain	0.00 RPM	6.04 RPM
SRP017611_kidney	0.00 RPM	5.16 RPM
SRP017611_liver	0.00 RPM	4.44 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2276 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2276 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,