RetrogeneDB ID: retro_mmus_3558

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:162697636..162698047(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082571
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sec22b
• Ensembl ID: ENSMUSG00000027879
• Aliases: None
• Description: SEC22 vesicle trafficking protein homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1338759]

Sequence

>retro_mmus_3558
GCCTGTGTGGCTGACGGGCTTCCGCTGGCCACCTCGATGCAGGAGGACAAGCAGTCAGGCCGGGACCTTCAACAGTATCA
GAGTCAGGCTAAGCAACTCTTTTGAAAGCTGAATGAGCAGTCTCCTACCAGATATACCTTGGAAACAGGAGCCATGACTT
TTCACTACAATAATGAGCAGGAGGTGTGTTACTTGGTTTTGTGTGAAGCCGCCTTCCCTAAGAAGTTGGCCTTTGCCTAC
CTAGAAGACTTGCACTCAGAATCTGATGAATAACATGGGAAGAAGGTGCCCACTGTGTCTAGGCCCTATTCCTTCATTGA
GTTTGATACCTTCATTCAGAAAACCAAGAAACTCTACATTGATAGCTGTGCTCAGAGAAATCTAGGCTCCATCAACACCG
AATTGCAAGAT

Alignment

ORF - retro_mmus_3558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.51 %
• Parental protein coverage: 82.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEA
          A.VADGLPLA.SMQED.QSGRDLQQYQSQAKQLF.KLNEQSPTR.TLE.GAMTFHY..EQ.VCYLVLCEA
Retrocopy ACVADGLPLATSMQEDKQSGRDLQQYQSQAKQLF*KLNEQSPTRYTLETGAMTFHYNNEQEVCYLVLCEA

Parental  AFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYIDSRARRNLGSINTELQD
          AFPKKLAFAYLEDLHSE.DE.HGKKVPTVSRPYSFIEFDTFIQKTKKLYIDS.A.RNLGSINTELQD
Retrocopy AFPKKLAFAYLEDLHSESDE*HGKKVPTVSRPYSFIEFDTFIQKTKKLYIDSCAQRNLGSINTELQD

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	52.64 RPM
SRP007412_cerebellum	0.00 RPM	46.37 RPM
SRP007412_heart	0.00 RPM	28.48 RPM
SRP007412_kidney	0.00 RPM	38.75 RPM
SRP007412_liver	0.03 RPM	38.37 RPM
SRP007412_testis	0.00 RPM	25.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3558 was not detected

EST

No EST(s) were mapped for retro_mmus_3558 retrocopy.

TSS

No TSS is located nearby retro_mmus_3558 retrocopy 5' end.

Lab

retro_mmus_3558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000027879	1 retrocopy	retro_mmus_3558 ,