RetrogeneDB ID: retro_mmus_1761

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:30495003..30495375(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000055771
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Bloc1s1
• Ensembl ID: ENSMUSG00000090247
• Aliases: Bloc1s1, AI839753, BLOS1, Gcn5l1
• Description: biogenesis of lysosome-related organelles complex-1, subunit 1 [Source:MGI Symbol;Acc:MGI:1195276]

Sequence

>retro_mmus_1761
ATGCTGTCCCGCTTGCTCAAAGAACACCAAGCCAAGCAGAACGAACGCAAGGAGCTGCAGGAGAAGAGGAGAGAAGCTAT
CGCTGCAGCGACCTGCCTGACCGAAGCGTTGGTGGATCACCTCAACGTGGGTGTAGCCCAGGCCTACATGAACCAGAGAA
AGCTGGACCATGAGGTGAAGACCCTACAGGTCCAGGCTGCCCAGTTTGCCAAGCAGACAGGCCAGTGGATTGGAATGGTG
GAGAACTTCAACCAGGCGCTTAAGGAAATTGGGGATGTGGAGAACTGGGCTAGGAGCATCAAGCTGGACATGTGCACCAT
TGCCACCGCGCTGGAATACGTCTACAAAGGGCAGCTGCAGTCTGCACCATCC

Alignment

ORF - retro_mmus_1761 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSRLLKEHQAKQNERKELQEKRRREAIAAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF
          MLSRLLKEHQAKQNERKELQEK.RREAIAAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF
Retrocopy MLSRLLKEHQAKQNERKELQEK-RREAIAAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF

Parental  AKQTGQWIGMVENFNQALKEIGDVENWARSIELDMRTIATALEYVYKGQLQSAPS
          AKQTGQWIGMVENFNQALKEIGDVENWARSI.LDM.TIATALEYVYKGQLQSAPS
Retrocopy AKQTGQWIGMVENFNQALKEIGDVENWARSIKLDMCTIATALEYVYKGQLQSAPS

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	0.09 RPM	2.45 RPM
SRP007412_cerebellum	0.04 RPM	4.43 RPM
SRP007412_heart	0.19 RPM	9.59 RPM
SRP007412_kidney	0.23 RPM	4.74 RPM
SRP007412_liver	0.11 RPM	5.54 RPM
SRP007412_testis	0.05 RPM	2.24 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1761 was not detected

EST

No EST(s) were mapped for retro_mmus_1761 retrocopy.

TSS

No TSS is located nearby retro_mmus_1761 retrocopy 5' end.

Lab

retro_mmus_1761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1761 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000061	1 retrocopy	retro_cfam_1156,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Mus musculus	ENSMUSG00000090247	1 retrocopy	retro_mmus_1761 ,
Otolemur garnettii	ENSOGAG00000010506	1 retrocopy	retro_ogar_786,