RetrogeneDB ID: retro_mmus_3526

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:136545085..136545987(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083828
• 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_3526
AGATGTGCCTTGATCCCACCCCTAGGGGAAACAGTCTTTTATCCTTGCCCTTAGCTTATAAGAACTCCAGTGAAGCCCAT
TTTCTTCACTACTGTGTTCACAGGCTGTGCGTTTGGATCAGCTGCTATTTGGCAGTTTGAGCCACTGAAGTCCAAGGTGC
AGCATTGTGTTGATGTCATAAAGCTATTTGGCTGGATAGCATACGGGCACAAAAAGAAGTAGACCTCAGAAAGGAGATTA
ACACACAGTGCAATAGCCTAGGTGATGGCGAGAAGACTGTGACAGGCATCATAGCTGCAGACGCCCTTGTATTCTGATTA
TGGAGAGTGTGGTTTCTGTGTCTGACCATGTCAGATGTTTCACATTCAAACCCACAATCTAGGGTCCTTTGGTCTCCAAT
ATGGCTGTCGATGTTCAGTCATTTCTTCTTATTCCACATGGCACAAATATATGTGTTGTGTGGAACTTCTCATCCAGCAT
TGTGAACAGGCTGGTTCAAGAGCAGTTTGTTCCCGTGTGCCTGTCTGAAGGTGTCCCTTCCAATTTTGTCAGTTATGTGT
GTAAAGTTGCCACAGGAAGATAAGGACCTACAGTTGGCACATTGGGAGCAATCATGACAATTCATGCTGCCATCTGCACC
AAGATCCCTGGGGGGAGGCTCGCTATCATCTTCCTCCCCGTTCTCCCATTCATGGTAGGCAATGCCTTAAAAGCCATCAT
TGCCATGGATACATCTGGGGTGATCCTGGGATGGAAACTTTTGACTATGGAGCTGCATCATGGCGAGGTCTCTTAGGATA
TAGTATATCATGTACTGTCATGAATTCATTTGGAAGAACAGGGAGCCTCTAGTGAAAGTCTGGTATAAAATAAGGACTAA
CAAACCCAAGAATGTAGATGGT

Alignment

ORF - retro_mmus_3526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.28 %
• Parental protein coverage: 80.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RSALIPPLEETVFYPSPYPIRTLVKPFFFTIGFTGCAFGSAAIWQYESLKSRVQSYFDGIK-ADWLDSIR
          R.ALIPPL.ETVFYP.P..IRT.VKP.FFT..FTGCAFGSAAIWQ.E.LKS.VQ...D.IK.A.WLDSIR
Retrocopy RCALIPPLGETVFYPCP*LIRTPVKPIFFTTVFTGCAFGSAAIWQFEPLKSKVQHCVDVIK<AIWLDSIR

Parental  PQKEGNLRKEINKWWNSLSDGQRTVTGIIAANALVFCLWRVPSLQRTMIRYFTSNPASKVLCSPMLLSTF
          .QKE..LRKEIN...NSL.DG..TVTGIIAA.ALVF.LWRV..L..TM.....SNP.S.VL.SP..LS.F
Retrocopy AQKEVDLRKEINTQCNSLGDGEKTVTGIIAADALVF*LWRVWFLCLTMSDVSHSNPQSRVLWSPIWLSMF

Parental  SHFSLFHMA-ANMYVLWSFSSSIVNILGQEQFVAVYLSAGVISNFVSYVCKVATGRYGPSLGASGAIMTV
          SHF.LFHMA..N..V.W.FSSSIVN.L.QEQFV.V.LS.GV.SNFVSYVCKVATGR.GP..G..GAIMT.
Retrocopy SHFFLFHMA<TNICVVWNFSSSIVNRLVQEQFVPVCLSEGVPSNFVSYVCKVATGR*GPTVGTLGAIMTI

Parental  LAAVCTKIPEGRLAIIFLPVFTFTAGNALKAIIAMDTAGMILGWKF-FDHAAHLGGALFG-IWYITYGHE
          .AA.CTKIP.GRLAIIFLPV..F..GNALKAIIAMDT.G.ILGWK..FD..A.....L.G.I.YI.Y.HE
Retrocopy HAAICTKIPGGRLAIIFLPVLPFMVGNALKAIIAMDTSGVILGWKL<FDYGAASWRGLLG<I*YIMYCHE

Parental  LIWKNREPLVKIWHEIRTNGPKKGGG
          .IWKNREPLVK.W..IRTN.PK...G
Retrocopy FIWKNREPLVKVWYKIRTNKPKNVDG

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	0.00 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 activity near the 5' end of retro_mmus_3526 was not detected

EST

No EST(s) were mapped for retro_mmus_3526 retrocopy.

TSS

No TSS is located nearby retro_mmus_3526 retrocopy 5' end.

Lab

retro_mmus_3526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3526 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,