RetrogeneDB ID: retro_mmus_1999

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:162907800..162908458(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082514
• 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_1999
TATTGTGCCAGCATCACCAGTGAGGAGGTACGAACACTAGAGGAACTCCTGAAGCCCCCAGAAGATGAAGGTGAACATTA
CAAAATTCCCCCACTAGGCAAACACGACTCCCAGCGCTGGGCCCAGGAGTATCTGCTAGAGCAGCAGAGAATGGGGCTCG
GGCAGCAAATGTGGCTGACAAGGAGAAAGGCCTCATAGGACCACTGGCGGAACTGGACACAAAAGATGTGGATGCCCTGC
TGAAGAAGTCTGAGCCCAGCATGAACAGCCAAAAGACGGATGTCCCTTTGGTGCCCTGACACAGCGCCTGCTGCAGGCCC
TAGTGGAGGAAAATATTATTTCCCCTATGGAGGACTCTTCTATTCCTGACATAGCTGGGAAAGAATCAGGGGCAGATGGA
GCAAGCACCTCCCCCTGCAATCAGAACAAGCCTTTCAGTTTGCCACATACTAAGTCCCTGGAGAGCCGCATCAAGGAGGA
GCTGATTGCCCAGGGCCTCCTGGAGTCCGAGGACCGGCCTGCGGAGGACGAGGTCCTTGCTGAGCTGAGCAAACGGCAGG
CTGAGCTGAAGGCACTCGGTGCACACAGCCGCACCAAGAAGCACGACCTGCTGAGGTTGGCAAAGGAGGCGGTGAGCTGG
CAGGAGCTAAGGCAGCGG

Alignment

ORF - retro_mmus_1999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.44 %
• Parental protein coverage: 51.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YCADITSEEVRTLEELLKPPEDEAEHYKIPPLGKHYSQRWAQEDLLEEQK-DGARAAAVADKKKGLIGPL
          YCA.ITSEEVRTLEELLKPPEDE.EHYKIPPLGKH.SQRWAQE.LLE.Q...GARAA.VADK.KGLIGPL
Retrocopy YCASITSEEVRTLEELLKPPEDEGEHYKIPPLGKHDSQRWAQEYLLEQQR<NGARAANVADKEKGLIGPL

Parental  TELDTKDVDALLKKSE-AQHEQPEDGCPFGALTQRLLQALVEENIISPMEDSPIPDMSGKESGADGASTS
          .ELDTKDVDALLKKSE.AQHEQP.DGCPFGALTQRLLQALVEENIISPMEDS.IPD..GKESGADGASTS
Retrocopy AELDTKDVDALLKKSE<AQHEQPKDGCPFGALTQRLLQALVEENIISPMEDSSIPDIAGKESGADGASTS

Parental  PRNQNKPFSVPHTKSLESRIKEELIAQGLLESEDRPAEDSEDEVLAELRKRQAELKALSAHNRTKKHDLL
          P.NQNKPFS.PHTKSLESRIKEELIAQGLLESEDRPAED...EVLAEL.KRQAELKAL.AH.RTKKHDLL
Retrocopy PCNQNKPFSLPHTKSLESRIKEELIAQGLLESEDRPAED---EVLAELSKRQAELKALGAHSRTKKHDLL

Parental  RLAKEEVSRQELRQR
          RLAKE.VS.QELRQR
Retrocopy RLAKEAVSWQELRQR

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	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	0.00 RPM	54.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1999 was not detected

EST

No EST(s) were mapped for retro_mmus_1999 retrocopy.

TSS

No TSS is located nearby retro_mmus_1999 retrocopy 5' end.

Lab

retro_mmus_1999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1999 has 0 orthologous retrocopies within eutheria group .

---

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,