RetrogeneDB ID: retro_mmus_713

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:54401091..54401964(+)
• Located in intron of: ENSMUSG00000020332

Retrocopy information

• Ensembl ID: ENSMUSG00000078151
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 3230401D17Rik
• Ensembl ID: ENSMUSG00000035399
• Aliases: Oser1, 3230401D17Rik, AI256769, Perit1
• Description: RIKEN cDNA 3230401D17 gene [Source:MGI Symbol;Acc:MGI:1913930]

Sequence

>retro_mmus_713
ATGAAATCCGAAGCCAAGGATGGAGAGGAGGAAAGTCTGCAAACTGCCTTCAAGAAATTAAGAGTGGACGCATCAGGGTC
CATCATATCTCTGTCTGTTGGAGAAGGCCCAAGTGTCAGAGCATCAGCCAGAACAGCAGCCGATGATACCAAACCGAAAA
CCATGTGTGCATCTAAAGACAGTTGGCATGGGTCTACAAGGAAGTCTTCACAAGGAGCAGTGAGAACCCAGCGTCGTAGA
CGGTCTAAGTCTCCTGTTCTTCATCCTCCCAAATTCATAAATTGCAGTACAACAGCACCTCCTTCCAGCAGCCAGCTTAA
GCACAGAAGCCAGACTGAGCCACCCGATGGCATCAGTGGACGGGGAATTTCAACACCCAAAGAGTTCAACGCAGGAGAAA
ACTCTACTTCTCTTGATGTTAATCACACAGGAGCAGCCATCGAGCCTCTGAGAAGCTCGGTTCTGAGGCTCCCATCAGAG
AGTAAAACAGAAGAGCTCTCTGATGCTACCCAAGTCTCCCAAGAAAGTCTTACGGCTAACGATCTCTCTGACTTTCAATC
TGTTTCCAAGCTAAGTCAGGGCAAGCCATGTGTGTGTGTAGGCAAGGAGTGCCAGTGTAAGAGGTGGCATGACATGGAAG
TGTATTCCTTTTCAGGTCTGCAGAATGTCCCTCCTCTGGCCCCAGAACGAAGATCACTTGAGGACTACTCTCAGTCACTG
CACACCAGAACTCTGTCTGGCTCGCCTCGATCCTGTTCCGAGCAAGCTCGTGTCTATGTGGATGATGTGACCATTGAGGA
CCTAGCAGGCTACATGGAGTATTACTTGTATATCCCTAAGAAAATGTCCCACATGGCAGAGATGATGTACACC

Alignment

ORF - retro_mmus_713 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSEAKDGEEESLQTAFKKLRVDASGSIISLSVGEGPSVRASARTAADDTKPKTMCASKDSWHGSTRKSS
          MKSEAKDGEEESLQTAFKKLRVDASGSIISLSVGEGPSVRASARTAADDTKPKTMCASKDSWHGSTRKSS
Retrocopy MKSEAKDGEEESLQTAFKKLRVDASGSIISLSVGEGPSVRASARTAADDTKPKTMCASKDSWHGSTRKSS

Parental  RGAVRTQRRRRSKSPVLHPPKFIHCSTTAPPSSSQLKHRSQTEPPDGISGRGISTPKEFNAGENSTSLDV
          .GAVRTQRRRRSKSPVLHPPKFI.CSTTAPPSSSQLKHRSQTEPPDGISGRGISTPKEFNAGENSTSLDV
Retrocopy QGAVRTQRRRRSKSPVLHPPKFINCSTTAPPSSSQLKHRSQTEPPDGISGRGISTPKEFNAGENSTSLDV

Parental  NHTGAAIEPLRSSVLRLPSESKTEELSDATQVSQESLTANDLSDFQSVSKLSQGKPCVCVGKECQCKRWH
          NHTGAAIEPLRSSVLRLPSESKTEELSDATQVSQESLTANDLSDFQSVSKLSQGKPCVCVGKECQCKRWH
Retrocopy NHTGAAIEPLRSSVLRLPSESKTEELSDATQVSQESLTANDLSDFQSVSKLSQGKPCVCVGKECQCKRWH

Parental  DMEVYSFSGLQNVPPLAPERRSLEDYSQSLHTRTLSGSPRSCSEQARVYVDDVTIEDLAGYMEYYLYIPK
          DMEVYSFSGLQNVPPLAPERRSLEDYSQSLHTRTLSGSPRSCSEQARVYVDDVTIEDLAGYMEYYLYIPK
Retrocopy DMEVYSFSGLQNVPPLAPERRSLEDYSQSLHTRTLSGSPRSCSEQARVYVDDVTIEDLAGYMEYYLYIPK

Parental  KMSHMAEMMYT
          KMSHMAEMMYT
Retrocopy KMSHMAEMMYT

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	2.92 RPM
SRP007412_cerebellum	0.00 RPM	4.30 RPM
SRP007412_heart	0.03 RPM	2.65 RPM
SRP007412_kidney	0.00 RPM	3.97 RPM
SRP007412_liver	0.00 RPM	4.12 RPM
SRP007412_testis	0.23 RPM	41.03 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_713 was not detected

EST

3 EST(s) were mapped to retro_mmus_713 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE627692	54401093	54401231	97.9	135	3	132
BQ632986	54401450	54401685	99.2	232	2	230
CF104782	54401079	54401262	100	183	0	183

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_13720	463 libraries	106 libraries	447 libraries	48 libraries	8 libraries
TSS #2	TSS_13721	225 libraries	555 libraries	282 libraries	9 libraries	1 library

The graphical summary, for retro_mmus_713 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_713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_713 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
Choloepus hoffmanni	ENSCHOG00000008281	1 retrocopy	retro_chof_1318,
Echinops telfairi	ENSETEG00000013561	1 retrocopy	retro_etel_1755,
Mus musculus	ENSMUSG00000035399	1 retrocopy	retro_mmus_713 ,