RetrogeneDB ID: retro_mmus_1882

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:3686361..3686959(+)
• Located in intron of: ENSMUSG00000026655

Retrocopy information

• Ensembl ID: ENSMUSG00000081070
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Parl
• Ensembl ID: ENSMUSG00000033918
• Aliases: Parl, D16Ertd607e, PRO2207, PSARL1, PSENIP2, Psarl
• Description: presenilin associated, rhomboid-like [Source:MGI Symbol;Acc:MGI:1277152]

Sequence

>retro_mmus_1882
ATGGCGTTGCAAGGTTGGGCACAGCTAGGCTGGCGCTGTGGTCCGGCGTGGGCGCCTCCCTTGGGTGGCGGCTACCGGGA
GCTCTCTGCGACCCAGGCCCCGCAGCTGCTTGGACGCAGGTTTAACTTGTTTCTTCAGCAAACGTGTGGATTTAGAAAAG
CACCCAGGAAGGTTGAACCTCGAAGATCAGACCCAGGGTCAAGTGGAGAAGCATATAAGAGAAGTGCCTTGATCCCGCCT
CTGGAAGAAACAGTCTTTTACCCTCCCCCTGTCCTATAAGAACTCTTGTGAAGCCCTTTTTCTTCACCATTGAGTTCACA
GGCTGTGCATTTGGGTCAGCTGCTATTTGGCAGTATGAATCACTGAAATCCAGGGTGCAGAGTTATTTTGATGGCATAAA
AGCTGACTGGTTGGATAGTATATGGCCACAAAAGGAGGAAACCTCGGAAAGGAGATTAACAAGTGGTGGAATAGCCTAAG
TGATGGCCAGCGGACTGTGACCAGCATCATAGCTGCAAATGCCCTCGTGTTCTCCATGTGGAGAGTGCCATCCCTGCATC
GAACCATGGTCAGATACTTTACATCCAACCCAGCATCA

Alignment

ORF - retro_mmus_1882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.58 %
• Parental protein coverage: 53.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALQGWVQRGWRCGPAWAPPLGGGYRELSATQAPRLLGRRFNLFVQQKCGFRKAPRKVEPRRSDTGSSGE
          MALQGW.Q.GWRCGPAWAPPLGGGYRELSATQAP.LLGRRFNLF.QQ.CGFRKAPRKVEPRRSD.GSSGE
Retrocopy MALQGWAQLGWRCGPAWAPPLGGGYRELSATQAPQLLGRRFNLFLQQTCGFRKAPRKVEPRRSDPGSSGE

Parental  AYKRSALIPPLEETVFY-PSPYPIRTLVKPFFFTIGFTGCAFGSAAIWQYESLKSRVQSYFDGIKADWLD
          AYKRSALIPPLEETVFY.PSP.PIRTLVKPFFFTI.FTGCAFGSAAIWQYESLKSRVQSYFDGIKADWLD
Retrocopy AYKRSALIPPLEETVFY<PSPCPIRTLVKPFFFTIEFTGCAFGSAAIWQYESLKSRVQSYFDGIKADWLD

Parental  SIRPQKE-GNLRKEINKWWNSLSDGQRTVTGIIAANALVFCLWRVPSLQRTMIRYFTSNPAS
          SI.PQKE.GNL.KEINKWWNSLSDGQRTVT.IIAANALVF..WRVPSL.RTM.RYFTSNPAS
Retrocopy SIWPQKE<GNLGKEINKWWNSLSDGQRTVTSIIAANALVFSMWRVPSLHRTMVRYFTSNPAS

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	19.79 RPM
SRP007412_cerebellum	0.00 RPM	19.37 RPM
SRP007412_heart	0.00 RPM	36.36 RPM
SRP007412_kidney	0.10 RPM	33.80 RPM
SRP007412_liver	0.00 RPM	23.24 RPM
SRP007412_testis	0.00 RPM	33.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1882 was not detected

EST

No EST(s) were mapped for retro_mmus_1882 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_86843	424 libraries	50 libraries	507 libraries	78 libraries	13 libraries

The graphical summary, for retro_mmus_1882 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_1882 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1882 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021241	2 retrocopies	retro_cjac_1415, retro_cjac_2384,
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315,
Homo sapiens	ENSG00000175193	1 retrocopy	retro_hsap_3526,
Gorilla gorilla	ENSGGOG00000000416	1 retrocopy	retro_ggor_2384,
Myotis lucifugus	ENSMLUG00000004507	1 retrocopy	retro_mluc_883,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882 , retro_mmus_3526,
Nomascus leucogenys	ENSNLEG00000006072	1 retrocopy	retro_nleu_491,
Oryctolagus cuniculus	ENSOCUG00000007882	1 retrocopy	retro_ocun_541,
Otolemur garnettii	ENSOGAG00000006126	1 retrocopy	retro_ogar_648,
Pongo abelii	ENSPPYG00000014338	2 retrocopies	retro_pabe_2290, retro_pabe_2912,
Pan troglodytes	ENSPTRG00000015673	1 retrocopy	retro_ptro_2394,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380,