RetrogeneDB ID: retro_mmus_3497

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:102655950..102657060(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080899
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tada3
• Ensembl ID: ENSMUSG00000048930
• Aliases: Tada3, 1110004B19Rik, ADA3, AI987856, Tada3l
• Description: transcriptional adaptor 3 [Source:MGI Symbol;Acc:MGI:1915724]

Sequence

>retro_mmus_3497
AGGCAACTGGAAGTTGAACCCAGATCCTCACTGACTGGCAGGATAAGAAAGGGGACCGACGATTCATGAAGCTAGGTCGA
GACCATGAGCTTGGTACTCCCCCCAACCAAGGGAAACCCAAGAAGCAGAAACTGGAAGGGAAGACAGGACATGGCCAGTC
CCTGGCCCAGGACAACCCAAATCCAAAAACGTTCAATCCAAGATCCAGGAATATGAATTTACTGGTGACCCAATCGACGT
GCCTTGGATCCCCAAGAATGATGCTCCCAACAGGTTCTGGGCCTCTGTGGAGCCCTATTGTGCCGACATCACCAATGAGG
AGGTACGAACACTAGAGGAACTCCTGAAGCCCCCAGAAGATGAAGCTGAACATTATAAGATTCCCCCACTAGGGAAACAC
TACTCTCAGCGCTGGACCCAAGAGGATCTGCTAGAGCAGAAGGACGGGCTCGGGCAGCAGCTGTGGCTGACAAGAAGAAA
GGCCTCAAGGGACCACTGACAGAACTGGACACAAAAGATGTGGATGCTCTGCTGAAGAAGTCTGAGGCCCAGCATGAACA
GTCAGAAGACGGGTGTCCCTTCGGTGCCCTGACACAGCACCTGCTGCAGGTCCTAGTGGAGGAAAATATTATTTCCCCTA
TGGAGGACTCTCCTATTCCTGACATATCTGGGAAAGAGTCAGGGGCAGATGGAGCAAGCACCCCCCAATCCCCGCAATCA
GAACAAACCTTTCAGTGTGCCACATACCAAGTCCCTTGAGAGCCGCATCAAGGAGGAGCTGATTGCCCAGGGCCTCCTGG
AGTTCGAGGACCGGCCGCGGAGGACTCAGAGGATGAGGTCCTTGCTGAGCTGCACAAACAGCCGTCTGAGCTGAAGGCAC
TCAGTGCACACAACTGCACCAAGAAACACGACCCGCTGAGGCTGGCAAAGGAGGAGGTGAGCCGGCAGGAGCTAAGGCAG
CGGGTCCACATGGCAGACAATGAGGTCATGGATGCCTTCAGAAAGATCATGGCTGCCTGGCAGAAGAAGTGCACCCCTAC
AAAGAAGGAAAAGGACCAGGCCTGGAAGACACTGAAGGAGCGGGAAAGCATCCTGAAGCTCCTAGATGGG

Alignment

ORF - retro_mmus_3497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.59 %
• Parental protein coverage: 85.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RVLEAE-TQILTDWQDKKGDRRFLKLGRDHELGAPPKHGKPKKQKLEGKTGHG-PGPGPGRPKSKNVQPK
          R.LE.E.TQILTDWQDKKGDRRF.KLGRDHELG.PP..GKPKKQKLEGKTGHG.P.PGPG.PKSKNVQ.K
Retrocopy RQLEVE<TQILTDWQDKKGDRRFMKLGRDHELGTPPNQGKPKKQKLEGKTGHG<PVPGPGQPKSKNVQSK

Parental  IQEYEFTDDPIDVPRIPKNDAPNRFWASVEPYCADITSEEVRTLEELLKPPEDEAEHYKIPPLGKHYSQR
          IQEYEFT.DPIDVP.IPKNDAPNRFWASVEPYCADIT.EEVRTLEELLKPPEDEAEHYKIPPLGKHYSQR
Retrocopy IQEYEFTGDPIDVPWIPKNDAPNRFWASVEPYCADITNEEVRTLEELLKPPEDEAEHYKIPPLGKHYSQR

Parental  WAQEDLLEEQKDG-ARAAAVADKKKGLIGPLTELDTKDVDALLKKSEAQHEQPEDGCPFGALTQRLLQAL
          W.QEDLLE.QKDG.ARAAAVADKKKGL.GPLTELDTKDVDALLKKSEAQHEQ.EDGCPFGALTQ.LLQ.L
Retrocopy WTQEDLLE-QKDG<ARAAAVADKKKGLKGPLTELDTKDVDALLKKSEAQHEQSEDGCPFGALTQHLLQVL

Parental  VEENIISPMEDSPIPDMSG-KESGA-DGASTSPRNQNKPFSVPHTKSLESRIKEELIAQGLLESEDRP-A
          VEENIISPMEDSPIPD.SG.K..G....A...PRNQNKPFSVPHTKSLESRIKEELIAQGLLE.EDRP.A
Retrocopy VEENIISPMEDSPIPDISG>KSQGQMEQAPPNPRNQNKPFSVPHTKSLESRIKEELIAQGLLEFEDRP<A

Parental  EDSEDEVLAELRKRQAELKALSAHNRTKKHDLLRLAKEEVSRQELRQRVRMADNEVMDAFRKIMAARQKK
          EDSEDEVLAEL.K...ELKALSAHN.TKKHD.LRLAKEEVSRQELRQRV.MADNEVMDAFRKIMAA.QKK
Retrocopy EDSEDEVLAELHKQPSELKALSAHNCTKKHDPLRLAKEEVSRQELRQRVHMADNEVMDAFRKIMAAWQKK

Parental  RTPTKKEKDQAWKTLKERESILKLLDG
          .TPTKKEKDQAWKTLKERESILKLLDG
Retrocopy CTPTKKEKDQAWKTLKERESILKLLDG

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	22.12 RPM
SRP007412_cerebellum	0.00 RPM	19.19 RPM
SRP007412_heart	0.00 RPM	14.57 RPM
SRP007412_kidney	0.02 RPM	14.46 RPM
SRP007412_liver	0.00 RPM	8.88 RPM
SRP007412_testis	0.09 RPM	54.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3497 was not detected

EST

No EST(s) were mapped for retro_mmus_3497 retrocopy.

TSS

No TSS is located nearby retro_mmus_3497 retrocopy 5' end.

Lab

retro_mmus_3497 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3497 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005324	2 retrocopies	retro_cfam_2011, retro_cfam_2106,
Equus caballus	ENSECAG00000018186	1 retrocopy	retro_ecab_601,
Mus musculus	ENSMUSG00000048930	2 retrocopies	retro_mmus_1999, retro_mmus_3497 ,
Otolemur garnettii	ENSOGAG00000034225	1 retrocopy	retro_ogar_362,
Rattus norvegicus	ENSRNOG00000008597	2 retrocopies	retro_rnor_1273, retro_rnor_1479,