RetrogeneDB ID: retro_mmus_3553

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:157429415..157429835(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083841
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_3553
GCCCTGAAGACAAGGGGTAACACACCAAAATATGGACTCATTTTTCATTCCACCTTCATTGGCCGAGCAGCTGCAAAGAA
CAAGGGCCGTATCTCCCGATACCTAGCAAACAAATGCAATATTGCCTCGAGAATTGATTGCTTCTCTGAGGTCCCCACAA
GTGTATTTAGAGAAAAACTCCGAGAACAAATTGAGGAATGGCTGTCTTTCTATGAGACTGGAGAGATCCCACGTAAGAAC
CTGGATGTCATGAAGGAAGCTGTGGTTCAGGCAGAGGAAGCGACTGCTGAAATCACCAGAAAGCTGGAAAAACAGAAGAA
GCGCTTGAAGAAGAAAAAAAAAAAGCGACTGGTTGCACTGGCCCTGGCCTCGTCAGAAAACAGCAGTACCCCAGAAGAGT
GCGAGGGAGGAGATAGGTGC

Alignment

ORF - retro_mmus_3553 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 63.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALKTRGNTPKYGLIFHSTFIGRAAAKNKGRISRYLANKCSIASRIDCFSEVPTSVFGEKLREQVEERLSF
          ALKTRGNTPKYGLIFHSTFIGRAAAKNKGRISRYLANKC.IASRIDCFSEVPTSVF.EKLREQ.EE.LSF
Retrocopy ALKTRGNTPKYGLIFHSTFIGRAAAKNKGRISRYLANKCNIASRIDCFSEVPTSVFREKLREQIEEWLSF

Parental  YETGEIPRKNLDVMKEAVVQAEEAAAEITRKLEKQEKKRLKKEKKRLAALALASSENSSTPEECEGGDRC
          YETGEIPRKNLDVMKEAVVQAEEA.AEITRKLEKQ.K...K....RL.ALALASSENSSTPEECEGGDRC
Retrocopy YETGEIPRKNLDVMKEAVVQAEEATAEITRKLEKQKKRLKKXXXXRLVALALASSENSSTPEECEGGDRC

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	49.37 RPM
SRP007412_cerebellum	0.09 RPM	47.46 RPM
SRP007412_heart	0.00 RPM	18.15 RPM
SRP007412_kidney	0.04 RPM	18.17 RPM
SRP007412_liver	0.00 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_3553 was not detected

EST

No EST(s) were mapped for retro_mmus_3553 retrocopy.

TSS

No TSS is located nearby retro_mmus_3553 retrocopy 5' end.

Lab

retro_mmus_3553 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3553 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,