RetrogeneDB ID: retro_mmus_3568

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:5699729..5701884(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081232
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Larp4
• Ensembl ID: ENSMUSG00000023025
• Aliases: Larp4, DXErtd793, DXErtd793e
• Description: La ribonucleoprotein domain family, member 4 [Source:MGI Symbol;Acc:MGI:2443114]

Sequence

>retro_mmus_3568
ATGGCTTTGAAGCAGGTGACATCTAAAGGCACTGGTTTAAATCCTAATGCCAAAGTATGGCAAGAAATTCCTTCTGGAAA
TCCGGATGTCACTCCTGTAACTGAACCCTCTTGGCATGAAACTGCAGCCACATCTGGATCTCACCCTGAGGGCAATACAG
AACTTTCAGAAGATATGTGTAAGGAATATGAAGTAATGTATTCTCCATCTTGTGAAATCACAAGGAATACTGCAGATGTT
GAAGAGTCAGCTGATGGAATGATCTTAGGACCTGAAGACCTGAGTTACCAACTCTATGATGTTTCTAGAGAAAGCAGTTC
ATCAATTTCTACAGAAGATTTAAAAGAATGTCTGAAAAAACAATTGGAATTCTGTTTCTCACGAGAAAATTTATCAAAGG
ATCTTTACTTGATATCTCAAATGGATAGTGATCAGTTCATCCTGATATGGACGGTTGCCAACATGGAAGAAATAAAAAAA
ATTGACTACAAATACAGATTTAATTCTTGAAGTATTGAGATCTTCCCCTATGGTACAAGTTGATGAGAAGGGAGAAAAGG
TGAGACTAAGTCATAAACGATGTATTGTGATTCTCAGAGAGATTCCTGAGACAACGCCTGTAGAGGAAGTGAAAGCTTTG
TTTAAAAATGAAAACTGCCCCAAAGTGATAAGCTGTGAGTTTGCGCACAACAGCAACTGGTACATCACTTTCCAGTCAGA
CACAGATGCGCAGCAGGCTTTTAAATACTTAAGAGAAGAAGTTAAAACATTTCAGGGCAAGCCAATCATGGCAAGGATAA
AAGCCATCAATACATTTTTTGCTAAGAATGGTTATCGATTAATGGATTCTAGTATGTATACTCAACCTATTCAGACTCCT
ACCCAATATCCCTCACCAGTCTTCATGCAACCAGTGTATAATCCTCAGCAGTACTCAGTGTATAGTCTTGTGCCTCAGTC
TTGGTCTCCAAGTCCTGCACCTTACTTTGAAACACCACTGGCTCCCTTTCCCAATGATAGTTTTGTGAATGACTTTAGTT
CACCAGGATCTTACAAAACAAATGCTGCTGCTATGAATATGGGCTGACCATTCCCAAAAAATCCTGTGAAGCCTCATTTT
AGGTCATCCAGTGGTTCAGAACACTCAACAGAGGGCTCCGTGTCATTGGGAGATGGACCACTGAGCAGATCTAGTTCAAG
GATCTTTCTTTCTGAACGGCATAACCCAACAGTAACAGGGCAGCAGGAACAAACTTATCTTCCAAAGGAGGCTCCCATTT
TACAGATGGAACAGAATGGGGACTTTGGAAGAGGCAGACGAACTCTCTTCAGAGGCCGAAGGCGAAGGGATGATGACAGG
ATCCCAAGACCCCAACCTGCAGCAACTGAAGCCAAGGCTCCAACTCCGAAGTTTGACTTGCTTGCTACAAATTTCCCTCC
TTTACCTGGAAGCTCATCGAGAGTGCCAGATGAACTTGGTTTGGAGAATAGAATGTCTGATGTCGTTAAAGGTGTCTGCA
GAGAAAAGGACAGCAAGGACGTGCGAGTTAGTTGCCCAGTGCCTGGAGAGGACGGACAGACAGACTGCACTTCTGCGCCG
CTCAGCATAAGTCCTAGTTCTCCGTGTACAGCTGAGCCTCCTGTGTTAAGCACAACTCAGCAAGAGCAGGATCAGATGGA
GGACTCTGCTGTTCCAAAGGACACTCTCAACCCAGTAGCTGTGCCAGTGTCTTCTCCAACTGCCACAAAGCCATCCCCGG
CAAACACTGCTTCACCTTGCACTAGTAACATAAACCCACCGAGAGTGGTGGCCCTGCAGGAACCTCGAAAGTTAAGCTAT
GCTGAAGTGTGCCAGAAGCCTCCTAAAGAGCCATCTCCAGTTCTCCTACAGCCGCTGCGGGAACTCCGGTCTAATGCAGT
ATCCCCCACCAGAAATGAAGAGAACGGAGCTCCCGAGAAGCCTGTTGAGAAGCCGCATGAGAAACCAGAAACAAGGGCTA
GTAAGGATCATTCTGGCTTCCGAGGCAACACCATTCCCAGGGGAGCGGCTGGAAAAATCAGGGAACAGAGACGCCAGTTC
AGCCATAGGGCTACACCTCAGGGAGTGACTCGACGTAATGGGAAAGAGCAATACGTGCCACCCAGATCACCGAAG

Alignment

ORF - retro_mmus_3568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALEQVTSKGTGLNPNAKVWQEIPSGNPDGTPVTEPSWHETAATSGSHPEGHTELSEDMCKEYEVMYSPS
          MAL.QVTSKGTGLNPNAKVWQEIPSGNPD.TPVTEPSWHETAATSGSHPEG.TELSEDMCKEYEVMYSPS
Retrocopy MALKQVTSKGTGLNPNAKVWQEIPSGNPDVTPVTEPSWHETAATSGSHPEGNTELSEDMCKEYEVMYSPS

Parental  CETTRNTADVEESADGMILGPEDLSYQLYDVSGESSSAISTEDLKECLKKQLEFCFSRENLSKDLYLISQ
          CE.TRNTADVEESADGMILGPEDLSYQLYDVS.ESSS.ISTEDLKECLKKQLEFCFSRENLSKDLYLISQ
Retrocopy CEITRNTADVEESADGMILGPEDLSYQLYDVSRESSSSISTEDLKECLKKQLEFCFSRENLSKDLYLISQ

Parental  MDSDQFVPIWTVANMEEIKK-LTTNTDLILEVLRSSPMVQVDEKGEKVRPSHKRCIVILREIPETTPVEE
          MDSDQF..IWTVANMEE....LTTNTDLILEVLRSSPMVQVDEKGEKVR.SHKRCIVILREIPETTPVEE
Retrocopy MDSDQFILIWTVANMEEXXX>LTTNTDLILEVLRSSPMVQVDEKGEKVRLSHKRCIVILREIPETTPVEE

Parental  VKALFKNENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAINTFFAKNGYR
          VKALFKNENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAINTFFAKNGYR
Retrocopy VKALFKNENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAINTFFAKNGYR

Parental  LMDSSMYTQPIQTPTQYPSPVFMQPVYNPQQYSVYSLVPQSWSPSPAPYFETPLAPFPNGSFVNGFSSPG
          LMDSSMYTQPIQTPTQYPSPVFMQPVYNPQQYSVYSLVPQSWSPSPAPYFETPLAPFPN.SFVN.FSSPG
Retrocopy LMDSSMYTQPIQTPTQYPSPVFMQPVYNPQQYSVYSLVPQSWSPSPAPYFETPLAPFPNDSFVNDFSSPG

Parental  SYKTNAAAMNMGRPFPKNRVKPHFRSSSGSEHSTEGSVSLGDGPLSRSSSRIFLSERHNPTVTGQQEQTY
          SYKTNAAAMNMG.PFPKN.VKPHFRSSSGSEHSTEGSVSLGDGPLSRSSSRIFLSERHNPTVTGQQEQTY
Retrocopy SYKTNAAAMNMG*PFPKNPVKPHFRSSSGSEHSTEGSVSLGDGPLSRSSSRIFLSERHNPTVTGQQEQTY

Parental  LPKEAPILQMEQNGDFGRGRRTLFRGRRRRDDDRIPRPQPAATEAKAPTPKFDLLATNFPPLPGSSSRVP
          LPKEAPILQMEQNGDFGRGRRTLFRGRRRRDDDRIPRPQPAATEAKAPTPKFDLLATNFPPLPGSSSRVP
Retrocopy LPKEAPILQMEQNGDFGRGRRTLFRGRRRRDDDRIPRPQPAATEAKAPTPKFDLLATNFPPLPGSSSRVP

Parental  DELGLENRMSDVVKGVCREKDSEDVRVSCPVPAEDGQTDCTSAPLSISPSPPCTAEPPVLSTTQQEQDQM
          DELGLENRMSDVVKGVCREKDS.DVRVSCPVP.EDGQTDCTSAPLSISPS.PCTAEPPVLSTTQQEQDQM
Retrocopy DELGLENRMSDVVKGVCREKDSKDVRVSCPVPGEDGQTDCTSAPLSISPSSPCTAEPPVLSTTQQEQDQM

Parental  EDSAVPKDTLNPVAVPVSSPTATKPSPANTASPCTSNINPPRAVALQEPRKLSYAEVCQKPPKEPSPVLV
          EDSAVPKDTLNPVAVPVSSPTATKPSPANTASPCTSNINPPR.VALQEPRKLSYAEVCQKPPKEPSPVL.
Retrocopy EDSAVPKDTLNPVAVPVSSPTATKPSPANTASPCTSNINPPRVVALQEPRKLSYAEVCQKPPKEPSPVLL

Parental  QPLRELRSNAVSPTRNEENGAPEKPVEKPHEKPETRASKDHSGFRGNTIPRGAAGKIREQRRQFSHRATP
          QPLRELRSNAVSPTRNEENGAPEKPVEKPHEKPETRASKDHSGFRGNTIPRGAAGKIREQRRQFSHRATP
Retrocopy QPLRELRSNAVSPTRNEENGAPEKPVEKPHEKPETRASKDHSGFRGNTIPRGAAGKIREQRRQFSHRATP

Parental  QGVTRRNGKEQYVPPRSPK
          QGVTRRNGKEQYVPPRSPK
Retrocopy QGVTRRNGKEQYVPPRSPK

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	33.48 RPM
SRP007412_cerebellum	0.13 RPM	28.83 RPM
SRP007412_heart	0.06 RPM	41.12 RPM
SRP007412_kidney	0.38 RPM	57.83 RPM
SRP007412_liver	0.30 RPM	61.58 RPM
SRP007412_testis	0.23 RPM	26.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3568 was not detected

EST

No EST(s) were mapped for retro_mmus_3568 retrocopy.

TSS

No TSS is located nearby retro_mmus_3568 retrocopy 5' end.

Lab

retro_mmus_3568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000161813	1 retrocopy	retro_hsap_1483,
Myotis lucifugus	ENSMLUG00000012513	1 retrocopy	retro_mluc_1180,
Macaca mulatta	ENSMMUG00000008172	1 retrocopy	retro_mmul_2129,
Mus musculus	ENSMUSG00000023025	1 retrocopy	retro_mmus_3568 ,
Nomascus leucogenys	ENSNLEG00000017798	1 retrocopy	retro_nleu_2388,
Pan troglodytes	ENSPTRG00000004935	1 retrocopy	retro_ptro_1003,
Rattus norvegicus	ENSRNOG00000049091	1 retrocopy	retro_rnor_644,