RetrogeneDB ID: retro_mmus_1870

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:33668268..33668463(-)
• Located in intron of: ENSMUSG00000024766

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl33
• Ensembl ID: ENSMUSG00000029142
• Aliases: Mrpl33, 0610009M10Rik, L33mt, MRP-L33
• Description: mitochondrial ribosomal protein L33 [Source:MGI Symbol;Acc:MGI:2137225]

Sequence

>retro_mmus_1870
ATGGTGCCTTCTGCTGTCTCATTTGCAAAGAGCAAGTCAAAATCTATTCTGGTCAAACTGGTGTGCCAAACCAAGACAGG
TTTCTCCTTCATCCACAAAAGAAGCCAACTTTGAGAGAAGCTGACCCTTCTGCACTATGATCCAATGGTGAACAAAAAAC
TTATCCTTGTGGAACAGAAAAAAATATATGCCCTC

Alignment

ORF - retro_mmus_1870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLSAVSFAKSKSKTILVKLVSQAGTGFSFNHKRSRLREKLSLLHYDPIVNKKVLFVEQKKIRSL
          M..SAVSFAKSKSK.ILVKLV.Q..TGFSF.HKRS.L.EKL.LLHYDP.VNKK...VEQKKI..L
Retrocopy MVPSAVSFAKSKSKSILVKLVCQTKTGFSFIHKRSQL*EKLTLLHYDPMVNKKLILVEQKKIYAL

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	16.03 RPM
SRP007412_cerebellum	0.00 RPM	12.11 RPM
SRP007412_heart	0.00 RPM	34.59 RPM
SRP007412_kidney	0.00 RPM	28.87 RPM
SRP007412_liver	0.00 RPM	17.37 RPM
SRP007412_testis	0.00 RPM	17.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1870 was not detected

EST

No EST(s) were mapped for retro_mmus_1870 retrocopy.

TSS

No TSS is located nearby retro_mmus_1870 retrocopy 5' end.

Lab

retro_mmus_1870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1870 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015881	1 retrocopy	retro_dnov_190,
Echinops telfairi	ENSETEG00000003239	2 retrocopies	retro_etel_2106, retro_etel_322,
Mus musculus	ENSMUSG00000029142	2 retrocopies	retro_mmus_1869, retro_mmus_1870 ,