RetrogeneDB ID: retro_mmus_3066

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:102377840..102378337(-)
• Located in intron of: ENSMUSG00000030987

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mettl6
• Ensembl ID: ENSMUSG00000021891
• Aliases: None
• Description: methyltransferase like 6 [Source:MGI Symbol;Acc:MGI:1914261]

Sequence

>retro_mmus_3066
ATGGCTTCTTACAAAGGAACGGACTGCAAACAAGGATTCTTAGCACTGAAGAAAAGGAGAAACTGAAAAGAGACCAAGCT
TTGGTGTCTGCTTTTAAACAGCAAAAACTGGAAAAAGAGGCTCAGAAGAACTGGGACCTTTTTTATAAAAGAAACAGTAC
CATTTTTTTCAAGAACAGACACTGGACCACCAGAGAGTTTGAGGAGCTGAGATCATGTAGGGAGTATGAAGGTCAGAAAT
TGACTTTGTTGGAGGCTGGCTGTGGGGTTGGGAACTGTTTATTCCCACTTTTAGAAGAAGAATTGAATCTCTTTGCCTAT
GCCTGTGATTTTTCTCCAAGGGCAGTTGACTATGTGAGGCAACATCCTTTGTACACTGCAGAGAAATGCAAAGTATTCCA
ATGTGACCTCACCAGAGATGACCTTGACCACTTCCCACCAGAGTCTGTGGATGCCATTACATTGATCTTTGTGCTCTCAG
CCGCGCACCCTGAGAAG

Alignment

ORF - retro_mmus_3066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.07 %
• Parental protein coverage: 59.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASF-QRKGLQARILSTEEEEKLKRDQALVSAFKQQKLEKEAQKNWDLFYKRNSTNFFKDRHWTTREFEE
          MAS..QR.GLQ.RILSTEE.EKLKRDQALVSAFKQQKLEKEAQKNWDLFYKRNST.FFK.RHWTTREFEE
Retrocopy MASY<QRNGLQTRILSTEEKEKLKRDQALVSAFKQQKLEKEAQKNWDLFYKRNSTIFFKNRHWTTREFEE

Parental  LRSCREYEGQKLTLLEAGCGVGNCLFPLLEEDLNLFAYACDFSPRAVDYVKQHPLYNAERCKVFQCDLTR
          LRSCREYEGQKLTLLEAGCGVGNCLFPLLEE.LNLFAYACDFSPRAVDYV.QHPLY.AE.CKVFQCDLTR
Retrocopy LRSCREYEGQKLTLLEAGCGVGNCLFPLLEEELNLFAYACDFSPRAVDYVRQHPLYTAEKCKVFQCDLTR

Parental  DDLLDHVPPESVDAVTLIFVLSAVHPEK
          DD.LDH.PPESVDA.TLIFVLSA.HPEK
Retrocopy DD-LDHFPPESVDAITLIFVLSAAHPEK

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	0.02 RPM	14.25 RPM
SRP007412_cerebellum	0.00 RPM	13.11 RPM
SRP007412_heart	0.00 RPM	8.47 RPM
SRP007412_kidney	0.00 RPM	12.07 RPM
SRP007412_liver	0.00 RPM	9.18 RPM
SRP007412_testis	0.00 RPM	29.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3066 was not detected

EST

No EST(s) were mapped for retro_mmus_3066 retrocopy.

TSS

No TSS is located nearby retro_mmus_3066 retrocopy 5' end.

Lab

retro_mmus_3066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3066 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,