RetrogeneDB ID: retro_mmus_669

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:97200129..97200477(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sp140
• Ensembl ID: ENSMUSG00000070031
• Aliases: None
• Description: Sp140 nuclear body protein [Source:MGI Symbol;Acc:MGI:3702467]

Sequence

>retro_mmus_669
ACAAGTCAATGTGATCAGAAACTAAAAAGCACTGAATTGTGGCCACAGACAAACTCCTGGCGGGTGACTGGCAGCCAAAA
GATTGTGCAGAAAAGAACATCAGTTAGAAAAAGGACTGTGTCATGTGTTCCCCAACATGTGTGCCAGAAGAAAGACCTGG
AAGCAAGGATGGGAAGCAGCCAAGGAGAAGTTCTGGGCACCAGGAGGAACATTCCTGCAAGGAAACCCAAGAAGCAGAGA
AGAAAAAAGAAAGGTCACAACTGGTCAAAACCAAAATGGAGAAAGCCAATGAGTGTACAGAGAAAATGTGGCAGACTAGC
CTTTTGCCAGGCAGCTTTCAAGAGAAAG

Alignment

ORF - retro_mmus_669 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.68 %
• Parental protein coverage: 71.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNSCEQT-RQTRQEPQDDLPSSLRQEAGAQQPTREKKCSCVICSPTYV--PEDLEARMGSSQGECVGTRR
          ...C.Q....T...PQ.............Q..T...K...V.C.P..V....DLEARMGSSQGE..GTRR
Retrocopy TSQCDQKLKSTELWPQTNSWRVTGSQKIVQKRTSVRKRT-VSCVPQHVCQKKDLEARMGSSQGEVLGTRR

Parental  NIPARKPKKQRRKKKGHNWSKPRWRKPMSVQRKRGRIAFFQAAFKRK
          NIPARKPKKQRRKKKGHNWSKP.WRKPMSVQRK.GR.AF.QAAFKRK
Retrocopy NIPARKPKKQRRKKKGHNWSKPKWRKPMSVQRKCGRLAFCQAAFKRK

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	1.75 RPM
SRP007412_cerebellum	0.04 RPM	1.56 RPM
SRP007412_heart	0.03 RPM	1.31 RPM
SRP007412_kidney	0.00 RPM	3.23 RPM
SRP007412_liver	0.00 RPM	3.30 RPM
SRP007412_testis	0.00 RPM	0.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_669 was not detected

EST

No EST(s) were mapped for retro_mmus_669 retrocopy.

TSS

No TSS is located nearby retro_mmus_669 retrocopy 5' end.

Lab

retro_mmus_669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_669 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000070031	2 retrocopies	retro_mmus_668, retro_mmus_669 ,