RetrogeneDB ID: retro_ocun_1594

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018707:2302435..2303192(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTFR1
• Ensembl ID: ENSOCUG00000008165
• Aliases: None
• Description: mitochondrial fission regulator 1 [Source:HGNC Symbol;Acc:29510]

Sequence

>retro_ocun_1594
GGAAAGGATGCAGTGGCATCTTTTGATGACATTGGACGGCAGCCAGGGAAGAAGGGGAATGGTCAACAAGACTATGGACA
GAAGTCAGGTCAAGGCCACCCCTTCAGGGATGACCTTTCTTTCTTTGTGAAGTCCCCGAGCAGGCAGATTTCTGTAACAA
ACTTGTCTCGGGAAGAGGCACAGCTGAAGATACAGCAGCTGCAAATAAGGAAGCCCTGCAGGTCAGTGCACTTGAACTTA
CACCTCTGCAAGCACAGATTGACAAAGCTGTCACCCTGCAAGAGCAGCAAAGTCTCACTGCAAGTGACTTAGATGCTACC
ACAGCAGCATCCCTTCCCCCATCACCTCTACTGCTCCTGCCCACCATGGGTGCCCACCAAATTCTATCTGCCATTGATCT
GAATAAAGAGAAAAGTGAGAAGCCAATGCTGGAAAGACTTTGGATAACAAAGAAACCCAAAAGCCAAATATGCAAAAGAT
CCTTAAAGTTATGAACAGTGTGAAACTTTGGGCAGGAAAGATTCCAGAACAAGATAGAAAGTCCAAGCCAGTGGATACTA
CTGATCCTGGTGCCCTCACAGCAGAGGCTCTGTTAAAGAAATTTGCCTATTGGTATCAAAATATTGGCCAAGGTAAAGTT
GAAAAAGGAGTTTCAAAATATGAATCAGAGTCCACCTCAGAGACAGTGTTGTTTGGGCCACGTATGTTGAAGTCTACAGA
AAAAATTAAGGCTTTAATTGAAAATATCTAAAACTCC

Alignment

ORF - retro_ocun_1594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.83 %
• Parental protein coverage: 79.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GEDTVASLADVG-WVAKEEGECSTRLRTEVRSRPPLQ-DDLPFFEKPPGRQISSPNLSQEESQLK-TTTL
          G.D.VAS..D.G...A.EEGE.STRL.TEVRSRPPLQ.DDL.FF.K.P.RQIS..NLS.EE.QLK..T..
Retrocopy GKDAVASFDDIG<TAAREEGEWSTRLWTEVRSRPPLQ>DDLSFFVKSPSRQISVTNLSREEAQLK<DTAA

Parental  ANEEALQKICALENELAVLRAQIAKIVTLQEQQHLIAGDLDTTASVTTAAPPPPPPPPPPPPPPALHQSL
          AN.EALQ...AL..EL..L.AQI.K.VTLQEQQ.L.A.DLD.T....TAA..PP.P....P...A.HQ.L
Retrocopy ANKEALQ-VSAL--ELTPLQAQIDKAVTLQEQQSLTASDLDAT----TAASLPPSPLLLLPTMGA-HQIL

Parental  SAIDLIKERKEKKANAGKTLVKNNPK-KPDMPNMLEILKDMNSVKLRAVKRPEQDVKPKPVDATDPGALI
          SAIDL.KE..EK............PK.KP.M.....ILK.MNSVKL.A.K.PEQD.K.KPVD.TDPGAL.
Retrocopy SAIDLNKEKSEKPM-LERLWITKKPK<KPNMQ---KILKVMNSVKLWAGKIPEQDRKSKPVDTTDPGALT

Parental  AEALKKKFAYRYRNDSPGEVEKGVPKCESESTSDTVLFGPHMLKSTGKMKALIENVSNS
          AEAL.KKFAY.Y.N...G.VEKGV.K.ESESTS.TVLFGP.MLKST.K.KALIEN..NS
Retrocopy AEALLKKFAYWYQNIGQGKVEKGVSKYESESTSETVLFGPRMLKSTEKIKALIENI*NS

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	9.16 RPM
SRP017611_kidney	0.00 RPM	28.38 RPM
SRP017611_liver	0.00 RPM	16.49 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1594 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1594 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012281	1 retrocopy	retro_amel_1640,
Choloepus hoffmanni	ENSCHOG00000006664	3 retrocopies	retro_chof_1268, retro_chof_2700, retro_chof_483,
Dipodomys ordii	ENSDORG00000016322	1 retrocopy	retro_dord_293,
Homo sapiens	ENSG00000066855	1 retrocopy	retro_hsap_4849,
Macaca mulatta	ENSMMUG00000011263	1 retrocopy	retro_mmul_2590,
Mustela putorius furo	ENSMPUG00000009909	2 retrocopies	retro_mputfur_1244, retro_mputfur_894,
Oryctolagus cuniculus	ENSOCUG00000008165	1 retrocopy	retro_ocun_1594 ,
Pongo abelii	ENSPPYG00000018631	1 retrocopy	retro_pabe_3769,
Rattus norvegicus	ENSRNOG00000021359	1 retrocopy	retro_rnor_1821,
Tarsius syrichta	ENSTSYG00000010102	1 retrocopy	retro_tsyr_1899,