RetrogeneDB ID: retro_mmus_1358

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:77701301..77701637(+)
• Located in intron of: ENSMUSG00000071716

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ino80c
• Ensembl ID: ENSMUSG00000047989
• Aliases: Ino80c, D030070L09Rik
• Description: INO80 complex subunit C [Source:MGI Symbol;Acc:MGI:2443014]

Sequence

>retro_mmus_1358
AGTAAAATGGCGTCCTCAGAGTTAAGCTCGGGGCCTGTGGAGAAAGCTGCCAAGCCATTGCCATTTAAGGATCCCAACTT
TGTGCACTCCCATCATGGCGGTGCAGTAACTGGCAAGAAGAATAGAACTTGGAAGAACCTCAAACAGATCCTCGCTGCTG
AAAGTCCATTGCCATGACAACTAAAGGATCCTAACTACTTTATTGTTGGTGCTCCTTCGTCCTTTAAGCCAGGTAAGAAG
TATTCTGATGTTTCAGGCCTTCTTGCCAACTATACAGAGCCTCAGAGCAAGCTGCAGTTCAGCACTATTGAGGAATTCTC
CTACATTTGAAGGCTG

Alignment

ORF - retro_mmus_1358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 83.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKMASSELSSGPVEKAAKPLPFKDPNFVHSGHGGAVAGKKNRTWKNLKQILAAERALPWQLNDPNYFSID
          SKMASSELSSGPVEKAAKPLPFKDPNFVHS.HGGAV.GKKNRTWKNLKQILAAE..LP.QL.DPNYF...
Retrocopy SKMASSELSSGPVEKAAKPLPFKDPNFVHSHHGGAVTGKKNRTWKNLKQILAAESPLP*QLKDPNYFIVG

Parental  APPSFKPAKKYSDISGLLANYTDPQSKLRFSTVEEFSYIRRL
          AP.SFKP.KKYSD.SGLLANYT.PQSKL.FST.EEFSYI.RL
Retrocopy APSSFKPGKKYSDVSGLLANYTEPQSKLQFSTIEEFSYI*RL

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	17.38 RPM
SRP007412_cerebellum	0.00 RPM	14.89 RPM
SRP007412_heart	0.03 RPM	18.30 RPM
SRP007412_kidney	0.00 RPM	24.49 RPM
SRP007412_liver	0.00 RPM	9.83 RPM
SRP007412_testis	0.00 RPM	53.15 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1358 was not detected

EST

No EST(s) were mapped for retro_mmus_1358 retrocopy.

TSS

No TSS is located nearby retro_mmus_1358 retrocopy 5' end.

Lab

retro_mmus_1358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1358 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021025	1 retrocopy	retro_cjac_922,
Myotis lucifugus	ENSMLUG00000030708	3 retrocopies	retro_mluc_118, retro_mluc_1892, retro_mluc_1942,
Mus musculus	ENSMUSG00000047989	2 retrocopies	retro_mmus_1358 , retro_mmus_1410,