RetrogeneDB ID: retro_mmus_786

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:46451077..46451383(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082530
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam104a
• Ensembl ID: ENSMUSG00000041629
• Aliases: Fam104a, D11Wsu99e
• Description: family with sequence similarity 104, member A [Source:MGI Symbol;Acc:MGI:106351]

Sequence

>retro_mmus_786
GGGGTGGCGCCGCGTCGCTCGCCTTCACCAGCTGCCATGAGCGAGCGCCTCCGCCCCAGAAAAAGGAGAAGAAATGGCAG
TGATGATGACAACCACCCTCCTCCCCAGACCAAAAGGAGCAGTAGGAACCCCATCTTCCAGGACTCCTGGGACACAGAGT
CTTCAAGCAGCGACAGTAGTGGGAGCAGCAGCAGCAGCAGCATCAACAGCCCAGACAGGGCCAGTGGGCCAGAGAGCAGC
CTGAGCCACACCATCCCCGGATCCTGCCCCAGCACCCCCACACACACGCCCCCCAGCCGATGCCTG

Alignment

ORF - retro_mmus_786 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.57 %
• Parental protein coverage: 55.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAAPRRSPSPAAMSERLRPRKRRRNGSDDDNHPPPQTKRSSRNPIFQDSWDTESSSSDSGGSSSSSSINS
          G.APRRSPSPAAMSERLRPRKRRRNGSDDDNHPPPQTKRSSRNPIFQDSWDTESSSSDS.G.........
Retrocopy GVAPRRSPSPAAMSERLRPRKRRRNGSDDDNHPPPQTKRSSRNPIFQDSWDTESSSSDSSGXXXXXXXXX

Parental  PDRASGPESSLSHTIPGSCPSTPQPMPEQSAL
          ...........SHTIPGSCPSTP...P....L
Retrocopy XXXXXXXXXXXSHTIPGSCPSTPTHTPPSRCL

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	12.59 RPM
SRP007412_cerebellum	0.00 RPM	14.29 RPM
SRP007412_heart	0.00 RPM	9.90 RPM
SRP007412_kidney	0.00 RPM	11.22 RPM
SRP007412_liver	0.00 RPM	8.22 RPM
SRP007412_testis	0.37 RPM	87.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_786 was not detected

EST

No EST(s) were mapped for retro_mmus_786 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_12853	346 libraries	581 libraries	137 libraries	3 libraries	5 libraries

The graphical summary, for retro_mmus_786 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_786 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_786 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002692	1 retrocopy	retro_amel_273,
Mus musculus	ENSMUSG00000041629	1 retrocopy	retro_mmus_786 ,
Oryctolagus cuniculus	ENSOCUG00000003744	1 retrocopy	retro_ocun_629,