RetrogeneDB ID: retro_mmus_3330

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:36813128..36813907(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nop56
• Ensembl ID: ENSMUSG00000027405
• Aliases: Nop56, 2310044F10Rik, Nol5a
• Description: NOP56 ribonucleoprotein [Source:MGI Symbol;Acc:MGI:1914384]

Sequence

>retro_mmus_3330
AGTGATTCCCAGGGCCCAGCAAAAGGGGACCGAGTTTCCAGAGCCCTGAAGACAAGGGGTAACACACCAAAATATAGACT
CATTTTTCATTCCACCTTCATTGGCCGAGCAGCTGCAAAGAACAAAGGCCGTATCTCCCGATACCTAGCAAACAAATGCA
GTATTGCCTCGAGAATTGATTGCTTCTCTGAGGTCCCCACAAGTGTATTTGGGGAAAAACTCCGAGAACAAGTTGAGGAA
CGGCTGTCTTTCTATGAGACTGGAGAGATCCCACGGAAGAACCTGGATGTCATGAAGGAAGCTGTGGTTCAGGCAGAGGA
AGCGGCTGCTGAAATCACCAGAAAGCTGGAAAAACAGGAGAAGAAGCACTTGAAGAAGGAAAAGAAGCGACTGGCTGCAC
TGGCCCTGGCCTCGTCAGAAAACAGCAGTACCCCAGAGGAGTGTGAGGAGGTACATGAAAAATCTAAGAAGAAGAAGTTA
AAACCCCAGGAGACCCTACAGGAAAATGGAATGGAAGACCCACCTGTCTCTCTACCTAAAACCAAGAAAAAGAAAGCTCC
CAAGGAGGAGTTGGCCAGTGACCTTGAAGAGATGGCCACTAGCAGTGCAAAGAGAAAGAAGTCCTCACCTAAGGAGGAAG
TGGCCAGTGAACCAGAAGAGGCAGCAAGCCCACCACCCCTAAAAAGAAAAGGAAATTTTCTGAGGAGCCTGAAGTTGCTG
CTAACTTCACAAAGAGCAGCACAAAGAAAAAGAAAAAGTCCCAGAAAACACAGGAGGAT

Alignment

ORF - retro_mmus_3330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.8 %
• Parental protein coverage: 86.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDSQGPAKGDRVSRALKTRGNTPKYGLIFHSTFIGRAAAKNKGRISRYLANKCSIASRIDCFSEVPTSVF
          SDSQGPAKGDRVSRALKTRGNTPKY.LIFHSTFIGRAAAKNKGRISRYLANKCSIASRIDCFSEVPTSVF
Retrocopy SDSQGPAKGDRVSRALKTRGNTPKYRLIFHSTFIGRAAAKNKGRISRYLANKCSIASRIDCFSEVPTSVF

Parental  GEKLREQVEERLSFYETGEIPRKNLDVMKEAVVQAEEAAAEITRKLEKQEKKRLKKEKKRLAALALASSE
          GEKLREQVEERLSFYETGEIPRKNLDVMKEAVVQAEEAAAEITRKLEKQEKK.LKKEKKRLAALALASSE
Retrocopy GEKLREQVEERLSFYETGEIPRKNLDVMKEAVVQAEEAAAEITRKLEKQEKKHLKKEKKRLAALALASSE

Parental  NSSTPEECEEVNEKSKKKKKLKPQE----NGMEDPPVSLPKSKKKKAPKEELASDLEEMATSSAKRKKSS
          NSSTPEECEEV.EKS.KKKKLKPQE....NGMEDPPVSLPK.KKKKAPKEELASDLEEMATSSAKRKKSS
Retrocopy NSSTPEECEEVHEKS-KKKKLKPQETLQENGMEDPPVSLPKTKKKKAPKEELASDLEEMATSSAKRKKSS

Parental  PKEEVASEPEEAAS-PTTPKKKRKFSEEPEVAANFTKSSTKKKKKSQKAQED
          PKEEVASEPEEAAS.PTTPKKKRKFSEEPEVAANFTKSSTKKKKKSQK.QED
Retrocopy PKEEVASEPEEAAS<PTTPKKKRKFSEEPEVAANFTKSSTKKKKKSQKTQED

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	49.37 RPM
SRP007412_cerebellum	0.00 RPM	47.46 RPM
SRP007412_heart	0.00 RPM	18.15 RPM
SRP007412_kidney	0.02 RPM	18.17 RPM
SRP007412_liver	0.03 RPM	19.31 RPM
SRP007412_testis	0.00 RPM	9.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3330 was not detected

EST

No EST(s) were mapped for retro_mmus_3330 retrocopy.

TSS

No TSS is located nearby retro_mmus_3330 retrocopy 5' end.

Lab

retro_mmus_3330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3330 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000027405	4 retrocopies	retro_mmus_1803, retro_mmus_3330 , retro_mmus_3553, retro_mmus_3574,