RetrogeneDB ID: retro_mmus_241

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:60155608..60156103(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000047370
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ubald2
• Ensembl ID: ENSMUSG00000050628
• Aliases: Ubald2, 1110014K08Rik, D030012E24Rik, Fam100b
• Description: UBA-like domain containing 2 [Source:MGI Symbol;Acc:MGI:1914635]

Sequence

>retro_mmus_241
ATGTCGGTGAACACGGACGAGCTGCGGCACCAGGTCATGATCAACCAGTTCGTGCTGGCCGCGGGCTGCGCGGCCGATCA
GGCGCAGCAGCTGCTGCAAGCGGCGCACTGGCAGTTCGAGACCGCCCTAAGCACGTTCTTTCAAGAAAGCAACATTCCCA
ACAGCCACCACCACCCGCAGATGATGTGTACCCCCAGCAACACCCCTGCTACACCACCCAACTTCCCTGATGCATTGGCC
ATGTTCTCCAAGCTTCGAACCTCTGAGGGCCTGCAGAGCAGCAGCAGCAGCCCCATGGCAGCCGTGGCCTGTTCCCCCCC
TGCAAACTTCAGCCCCTTCTGGGCCGCATCCCCACCCAATCACCAGGTGCCCTGGATCCCGCCCTCTTCCCCCAACACCT
TCCATCTCCACTGCCCACAGCCCACGTGGCCCCCCAGAGCATCGCAGGGGGGCGCCCCTCAGAAAGCCATGGCAGCCATG
GATGGCCAGAGATGA

Alignment

ORF - retro_mmus_241 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVNTDELRHQVMINQFVLAAGCAADQAQQLLQAAHWQFETALSTFFQESNIPNSHHHPQMMCTPSNTPA
          MSVNTDELRHQVMINQFVLAAGCAADQAQQLLQAAHWQFETALSTFFQESNIPNSHHHPQMMCTPSNTPA
Retrocopy MSVNTDELRHQVMINQFVLAAGCAADQAQQLLQAAHWQFETALSTFFQESNIPNSHHHPQMMCTPSNTPA

Parental  TPPNFPDALAMFSKLRTSEGLQSSSSSPMAAVACSPPANFSPFWAASPPNHQVPWIPPSSPNTFHLHCPQ
          TPPNFPDALAMFSKLRTSEGLQSSSSSPMAAVACSPPANFSPFWAASPPNHQVPWIPPSSPNTFHLHCPQ
Retrocopy TPPNFPDALAMFSKLRTSEGLQSSSSSPMAAVACSPPANFSPFWAASPPNHQVPWIPPSSPNTFHLHCPQ

Parental  PTWPPGASQGGAPQKAMAAMDGQR
          PTWPP.ASQGGAPQKAMAAMDGQR
Retrocopy PTWPPRASQGGAPQKAMAAMDGQR

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	2.22 RPM
SRP007412_cerebellum	0.00 RPM	0.69 RPM
SRP007412_heart	0.03 RPM	4.64 RPM
SRP007412_kidney	0.12 RPM	3.70 RPM
SRP007412_liver	0.08 RPM	1.97 RPM
SRP007412_testis	0.09 RPM	2.97 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_241 was not detected

EST

1 EST(s) were mapped to retro_mmus_241 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA061475	60155746	60155919	99.5	172	1	171

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_136443	459 libraries	512 libraries	97 libraries	4 libraries	0 libraries

The graphical summary, for retro_mmus_241 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_241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_241 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
Mus musculus	ENSMUSG00000039568	1 retrocopy	retro_mmus_3365,
Mus musculus	ENSMUSG00000050628	1 retrocopy	retro_mmus_241 ,
Rattus norvegicus	ENSRNOG00000010029	1 retrocopy	retro_rnor_1380,