RetrogeneDB ID: retro_rnor_1273

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:58916942..58918241(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Tada3
• Ensembl ID: ENSRNOG00000008597
• Aliases: Tada3, Tada3l
• Description: Transcriptional adapter 3 [Source:UniProtKB/Swiss-Prot;Acc:Q4V8F5]

Sequence

>retro_rnor_1273
ATGAGTGAATTGAAGGACTGCCCATTGCAGTTTCATGACTTCAAGTCTGTGGACCACCTGAAGGTCTGTCCCAGGTACAC
GGCAGTGCTGGCCCACTCTGAGGATGATGGCATTGGCATCGAGTAGCTGGACACCCTGCAGCTGGAGCTTGAGACCCTGC
TATCCTCTGCAAGCAGGCGACTGCGTGTACTGGAAGCTGAAACCCAGATCCTTACTAACTGGCAGGATAAGAAAGGTGAC
AGGTGATTTTTGAAGCTTGGTCGAGACCATGAGCTTGGTGTCCCCCCAAAACATGGGAAGCACAAGAAGCAGAAACTGTA
AGGGAAGACAGGACATGGGCCAAGCCCTGGCCCAGGACGACCCAAATCCAAAAATGTTCAACCCAAGATCCAGAAATATT
AATTTACTGATGACCCAATTGATGTGCCTCGGATCCCCAAGAACGATGCTCCCAACAGGTTCTGGGCCTCTGTGGAGCCC
TATTGTGCCAACATCACTAGTGAGGAGGTACGAACACTAGAGGAGCTCCTGAAGCCCCCTAAAGATGAAGCTGAACATTA
TAAGATTCCCCCACTAGGGAAACATTACTCCCAACGCTGGTCCCAGGAGGATCTGCTAGAGGAGCAGAAAGATGTGACTC
AAGCAGCAGCTGTGGCTGACAAGAAGAAAGGCCTCATAGAACTGCTGACAGAACTGGACACAAAAGATGTGGATGCCCTG
CTGAAGAAGTCTGAGGCCCAGCATGAACAGCCAGAAGACAGGTGTCCCTTTGGTGCCCTGACACAGCGCCTGCTGCAGGT
CCTCGTGGAGGAAAATATTATTTCCTCTATGGAGGACTCTCCAATTCCTGACATGTCTGGGAAAGAATCAGGGGCTGATG
GAGCGACACCCCCCTCACCCCGCAATCAGAACAAACCTTTCATTGTGCCACATACAAAGTCCTTGGAGAGCCGCATCAAG
GAGGAACTGATTGCCCAGGGCCTACTGGAGTCCGAGGACCGGCCTGCTGAGGACTCAGAGGATGAGGTCCTCGCTGAGCT
GCGCAAACGGCAGGCTGAGCTGAAGGCGCTCAGTGCACACAACCGTACCAAGAAGCACGACCTGCTGAGGTTGGCAAAGA
AGGAGGTGAGCCTGGAGGAGCTGAGGCAGCGGGTCCGCATGGCAGACAATGAGGTCATGGATGCCTTCCGCAAGATCATG
GCTGCGTGGCAGAAGAAGCGCACCCCCACAAAGAAGGAAAAGGACTAGGCCTGGAAGACCCTGAAGGATCGGAAGAGGAT
CCTGAAGCTCCTAGATGGG

Alignment

ORF - retro_rnor_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSELKDCPLQFHDFKSVDHMKVCPRYTAVLARSEDDGIGIEELDTLQLELETLLSSASRRLRVLEAETQI
          MSELKDCPLQFHDFKSVDH.KVCPRYTAVLA.SEDDGIGIE.LDTLQLELETLLSSASRRLRVLEAETQI
Retrocopy MSELKDCPLQFHDFKSVDHLKVCPRYTAVLAHSEDDGIGIE*LDTLQLELETLLSSASRRLRVLEAETQI

Parental  LTDWQDKKGDRRILKLARDHELGAPPKHGKPKKQKLEGKTGHGPGPGPGRPKSKNVQPKIQEYEFTDDPI
          LT.WQDKKGDR..LKL.RDHELG.PPKHGK.KKQKL.GKTGHGP.PGPGRPKSKNVQPKIQ.Y.FTDDPI
Retrocopy LTNWQDKKGDR*FLKLGRDHELGVPPKHGKHKKQKL*GKTGHGPSPGPGRPKSKNVQPKIQKY*FTDDPI

Parental  DVPRIPKNDAPNRFWASVEPYCADITSEEVRTLEELLKPPEDEAEHYKIPPLGKHYSQRWAQEDLLEEQK
          DVPRIPKNDAPNRFWASVEPYCA.ITSEEVRTLEELLKPP.DEAEHYKIPPLGKHYSQRW.QEDLLEEQK
Retrocopy DVPRIPKNDAPNRFWASVEPYCANITSEEVRTLEELLKPPKDEAEHYKIPPLGKHYSQRWSQEDLLEEQK

Parental  DGARAAAVADKKKGLIGPLTELDTKDVDALLKKSEAQHEQPEDGCPFGALTQRLLQALVEENIISPMEDS
          D...AAAVADKKKGLI..LTELDTKDVDALLKKSEAQHEQPED.CPFGALTQRLLQ.LVEENIIS.MEDS
Retrocopy DVTQAAAVADKKKGLIELLTELDTKDVDALLKKSEAQHEQPEDRCPFGALTQRLLQVLVEENIISSMEDS

Parental  PIPDMSGKESGADGAS-TSPRNQNKPFSVPHTKSLESRIKEELIAQGLLESEDRPAEDSEDEVLAELRKR
          PIPDMSGKESGADGA...SPRNQNKPF.VPHTKSLESRIKEELIAQGLLESEDRPAEDSEDEVLAELRKR
Retrocopy PIPDMSGKESGADGATPPSPRNQNKPFIVPHTKSLESRIKEELIAQGLLESEDRPAEDSEDEVLAELRKR

Parental  QAELKALSAHNRTKKHDLLRLAKEEVSRQELRQRVRMADNEVMDAFRKIMAARQKKRTPTKKEKDQAWKT
          QAELKALSAHNRTKKHDLLRLAK.EVS..ELRQRVRMADNEVMDAFRKIMAA.QKKRTPTKKEKD.AWKT
Retrocopy QAELKALSAHNRTKKHDLLRLAKKEVSLEELRQRVRMADNEVMDAFRKIMAAWQKKRTPTKKEKD*AWKT

Parental  LKERESILKLLDG
          LK.R..ILKLLDG
Retrocopy LKDRKRILKLLDG

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
SRP017611_brain	0.00 RPM	31.78 RPM
SRP017611_kidney	0.00 RPM	16.61 RPM
SRP017611_liver	0.00 RPM	11.30 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1273 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1273 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,