RetrogeneDB ID: retro_rnor_2733

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:56152311..56152929(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mettl6
• Ensembl ID: ENSRNOG00000019520
• Aliases: None
• Description: Methyltransferase-like protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q6AXU8]

Sequence

>retro_rnor_2733
TTGAAGAGCTAAGATCATTATGAAGGTTAAAAAATTGACTGTATTGGAAACTGGATATGGGGTTGGGAACTGTTTCTTCC
CATTTTTAGAAGAATATTTGAATATAATTGCCTATGCCTGTGATTTTTCTTCAACGGCAGTTGACTACATGTTGCAACAT
CCTTTGAACAGCGCAGAGAGATGCAAAGTGTTCCAGTGTAACCTCACTAAAGATGACCATGACCATGTCCCACCTGAGTC
TGTGGATGCCGTCACATTGATCTTTGGGCTCTCAGCTGTGTGCCCTGAGAAGACGCACCTCATCTTATGAAATGTGCACC
AGGTATTAAAACCAGGCAGAAATGTCTTGTTCCATGACTATGGGCTCAATGGTCATGCCATGCTTACATTTAAAGCTGGA
AGCCAGCCTGGAGAAAATTTCTATGTCAGACAAGATGGAAACAGATTGTGTGTTTTTACTGATGAATTCCTGGCATAGTT
GTTGGCAGATGCAGGCTATGAAGAAGTGGTGAATGAGGATGTGTTTCAAGAGACCGTGAGTACAAAAGAGGGCCTGTTTG
TGCCATGGGTTTCCTTCAGAGCAAGTTCTGGAAGCCTCTGAAGAACCCAGCACCTACC

Alignment

ORF - retro_rnor_2733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.68 %
• Parental protein coverage: 72.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRSCREYEG-QKLTLLEAGCGVGNCLFPLLEEDSNIFAYACDFSPRAVDYVKQHPLYNAERCKVFQCDLT
          L.S...YEG..KLT.LE.G.GVGNC.FP.LEE..NI.AYACDFS..AVDY..QHPL..AERCKVFQC.LT
Retrocopy LKS*DHYEG>KKLTVLETGYGVGNCFFPFLEEYLNIIAYACDFSSTAVDYMLQHPLNSAERCKVFQCNLT

Parental  RDDLLDHIPPESVDAVTLIFVLSAVHPEKMHLVLLNVYKVLKPGRSVLFRDYGLNDHAMLRFKAGSKLGE
          .DD..DH.PPESVDAVTLIF.LSAV.PEK.HL.L.NV..VLKPGR.VLF.DYGLN.HAML.FKAGS..GE
Retrocopy KDDH-DHVPPESVDAVTLIFGLSAVCPEKTHLIL*NVHQVLKPGRNVLFHDYGLNGHAMLTFKAGSQPGE

Parental  NFYVRQDGTRSYFFTDEFLAKLFVDAGYEEVVNEYVFRETVNKKEGLCVPRV-FLQSKFRKPPKDPAPT
          NFYVRQDG.R...FTDEFLA.L..DAGYEEVVNE.VF.ETV..KEGL.VP.V.FLQSKF.KP.K.PAPT
Retrocopy NFYVRQDGNRLCVFTDEFLA*LLADAGYEEVVNEDVFQETVSTKEGLFVPWV<FLQSKFWKPLKNPAPT

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	9.42 RPM
SRP017611_kidney	0.00 RPM	9.91 RPM
SRP017611_liver	0.00 RPM	9.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2733 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2733 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000021891	1 retrocopy	retro_mmus_3066,
Rattus norvegicus	ENSRNOG00000019520	1 retrocopy	retro_rnor_2733 ,