RetrogeneDB ID: retro_mmus_3287

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:70852575..70853415(+)
• Located in intron of: ENSMUSG00000032207

Retrocopy information

• Ensembl ID: ENSMUSG00000096160
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rrp7a
• Ensembl ID: ENSMUSG00000018040
• Aliases: None
• Description: ribosomal RNA processing 7 homolog A (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1922028]

Sequence

>retro_mmus_3287
ATGGTGTCTCGCAGGAAGAAACAGAAGGCTGGCGGCCACGAGGAGAGCATACCGAGCCCACCGGGGTATTCAGCTGTTCC
AGTCAAGTTCTCGGCAAAGCAGCAGGCTCCTCATTACCTCTACATGAGACAGCACCGAGTTTGCCAAGGCACCCAGTCCA
CATGGCCTCCCGATCGAACCTTTTTTATCCTTAATGTGCCCCCGTACTGCACACAGGAGAGCCTGTTTTGGTGCCTCTCC
TGTTGCGGCACCATCAAGACAGTGGAGCTGCAGGAGAAGCCCGACCTTGCCGAGAGCCCCACGGAGCCAAAGTCACAGTT
TTTCCATCCCAAGCCGGTGCCGGGCTTTCAGGTAGCTTATGTGGTGTTCCAGAAGCCAAGTGGAGTGTCGGCCGCCTTGA
ACCTGAAGGGCCTATTGCTGGTTTCTACAGAGAGCCACCTTGTGAAGAGCGGAATTCACAAGTGGATCAGCGACTATGAA
GACTCCGTGCTGGACCCTGAGGCCCTGAGAATGGAAGTAGACGCATTCATGGAGGCCTATGACAAGAAGATAGCTGAGGA
GGAGGCTAAGGCCAAGGAGGAGGAGGGAGTCCCTGACGAGGAGGGCTGGGTGAAGGTCACCCGCCGGGGCTGCAGGCCAA
TGCTCCCTCAGACGGAAGCCGCCAGCCTGCGTGTTCTGGAGAAGGAGAAACGGAAGCGTGCCCGCAAGGAGCTGCTCAAC
TTCTATGCCTGGCAGCACCGAGAGACCAAGATGGAGCACCTGGCACAGCTGCGAAAGAAGTTTGAGGAGGACAAGCAGAG
GATTGAACTGATGCGGGCCCAGCGTAAATTCCGACCCTAC

Alignment

ORF - retro_mmus_3287 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSRRKKRKAGGHEESIPSPPGYSAVPVKFSAKQQAPHYLYMRQHRVRQGTQSTWPPDRTLFILNVPPYC
          MVSRRKK.KAGGHEESIPSPPGYSAVPVKFSAKQQAPHYLYMRQHRV.QGTQSTWPPDRT.FILNVPPYC
Retrocopy MVSRRKKQKAGGHEESIPSPPGYSAVPVKFSAKQQAPHYLYMRQHRVCQGTQSTWPPDRTFFILNVPPYC

Parental  TQESLSRCLSCCGTIKTVELQEKPDLAESPTEPKSQFFHPKPVPGFQVAYVVFQKPSGVSAALNLKGPLL
          TQESL..CLSCCGTIKTVELQEKPDLAESPTEPKSQFFHPKPVPGFQVAYVVFQKPSGVSAALNLKG.LL
Retrocopy TQESLFWCLSCCGTIKTVELQEKPDLAESPTEPKSQFFHPKPVPGFQVAYVVFQKPSGVSAALNLKGLLL

Parental  VSTESHLVKSGIHKWISDYEDSVLDPEALRMEVDAFMEAYDKKIAEEEAKAKEEEGVPDEEGWVKVTRRG
          VSTESHLVKSGIHKWISDYEDSVLDPEALRMEVDAFMEAYDKKIAEEEAKAKEEEGVPDEEGWVKVTRRG
Retrocopy VSTESHLVKSGIHKWISDYEDSVLDPEALRMEVDAFMEAYDKKIAEEEAKAKEEEGVPDEEGWVKVTRRG

Parental  RRPVLPRTEAASLRVLEKEKRKRARKELLNFYAWQHRETKMEHLAQLRKKFEEDKQRIELMRAQRKFRPY
          .RP.LP.TEAASLRVLEKEKRKRARKELLNFYAWQHRETKMEHLAQLRKKFEEDKQRIELMRAQRKFRPY
Retrocopy CRPMLPQTEAASLRVLEKEKRKRARKELLNFYAWQHRETKMEHLAQLRKKFEEDKQRIELMRAQRKFRPY

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	0.07 RPM	41.96 RPM
SRP007412_cerebellum	0.09 RPM	34.39 RPM
SRP007412_heart	0.09 RPM	19.21 RPM
SRP007412_kidney	0.19 RPM	29.07 RPM
SRP007412_liver	0.00 RPM	16.99 RPM
SRP007412_testis	0.09 RPM	57.40 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3287 was not detected

EST

No EST(s) were mapped for retro_mmus_3287 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_152778	364 libraries	105 libraries	230 libraries	287 libraries	86 libraries

The graphical summary, for retro_mmus_3287 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_3287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000018040	1 retrocopy	retro_mmus_3287 ,