RetrogeneDB ID: retro_rnor_1479

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:13312429..13313712(+)
• 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_1479
ATGAGTGAACTGAAGGACTGCCCATTGCAGTTTCATAACTTCAAGTCTGTGGACCACATGAATGTCTGTCCCCGGTACAC
GGCAGTGCTGGCCCGCTCCGAGGATGATGGCATTGGCATCGAGGAGCTGAACACCATGCAGCTGGAGCTTGAGACCCTGC
TGTCCTCTGCAAGCAGGCGACTGTGTGTACTGGAAGCTGAAATGCAGATCCTTACTGACTGGCAGGATAAGAAAGGTGAC
AGGAGAATTCTGAAGCTTGGTCGAGACCATGAGCTTGGTGCCCCCCACCCCCAAAACATGGGAAGCCCAAGAAGCAGAAA
CTGGAAAGGAAGACAGGACATGGGCCAGGCCTTGGCCCAAGACGACCCAAATCCAAAAATGTTCAACCCAAGATCTAGGA
ATATGAATTTACTGCTGACCCAATCGATGTGCCTCAGATCCCCAAGAACGATGCTCCCAACAGGCTCTGGGCTTCTGTGG
AGCCCTATTGTGCCGACATCACCAGTAAGGACGAACGAACACTAGTGGAGCTCTTGAAGCCCCCTGAAGATGAAGCTGAA
CATTATAAGATTCCCCCACTAGGTAAACACTACTCCCAACGCTGGGCCCAGGAGGATCTGCTAGAGGAGAAGGATGGGGC
TCGAGTAGCAGCTATGGCTGACAAGAAGAAAGGCCTTATAGGATCGCTGACAGAACTAGACACAAAAGATGTGGATGCCC
TGCTGAAGAAGTCTGAGGCCCAGCATGAACAGCCAGAAAACAGGTGTCCCTTTGGTGCCCTGACACAACGCCTGCTGCAG
GCCCTAGTGGAGGAAAATATTATTTCCCCTATGGAGGACTCTCCGATTCCTGACATGTCTGGGGAAGAATCAGGGGCTGA
TGGAGCGAGCACCTCCGCCCGCAATCAGAATAAACCTTTCAGTGTGCCACATACCAAGTCCTTGGAGAGCCGCATCAAAG
AGGAGCTGATTGCCCAGGACCTACTGGAGTCCGAGGACCGGCCTCCTGAGGACTCAGAGGATGAGGTCTTCGCTGTGCTG
CGCAAACGGCAGGCTGAGCTGAAGGCGCTCAGTGCACACAACCGCACCAAGAAGCACGACCTGCTGAGGTTGACAAAGGA
GGAGGTAAGCCGGCAAGAGCTGAGTCAGCGGGCCCGCATGGCAGACAATGAGGTCATGGATGCCTTCCGCAAGATCATGG
CTGCGCAGCAGAAGAAGCGTACCCCCACAAAGAAGGAAAAGGACCAGGCCTGGAAGACCCTGAAGGAACGGAAGAACATC
CTA

Alignment

ORF - retro_rnor_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSELKDCPLQFHDFKSVDHMKVCPRYTAVLARSEDDGIGIEELDTLQLELETLLSSASRRLRVLEAETQI
          MSELKDCPLQFH.FKSVDHM.VCPRYTAVLARSEDDGIGIEEL.T.QLELETLLSSASRRL.VLEAE.QI
Retrocopy MSELKDCPLQFHNFKSVDHMNVCPRYTAVLARSEDDGIGIEELNTMQLELETLLSSASRRLCVLEAEMQI

Parental  LTDWQDKKGDRRILKLARDHELGAP-PKH-GKP-KKQKLEGKTGHGPGPGPGRPKSKNVQPKIQEYEFTD
          LTDWQDKKGDRRILKL.RDHELGAP.P...G.P.KKQKLE.KTGHGPG.GP.RPKSKNVQPKI.EYEFT.
Retrocopy LTDWQDKKGDRRILKLGRDHELGAPHPQNMGSP<KKQKLERKTGHGPGLGPRRPKSKNVQPKI*EYEFTA

Parental  DPIDVPRIPKNDAPNRFWASVEPYCADITSEEVRTLEELLKPPEDEAEHYKIPPLGKHYSQRWAQEDLLE
          DPIDVP.IPKNDAPNR.WASVEPYCADITS...RTL.ELLKPPEDEAEHYKIPPLGKHYSQRWAQEDLLE
Retrocopy DPIDVPQIPKNDAPNRLWASVEPYCADITSKDERTLVELLKPPEDEAEHYKIPPLGKHYSQRWAQEDLLE

Parental  EQKDGARAAAVADKKKGLIGPLTELDTKDVDALLKKSEAQHEQPEDGCPFGALTQRLLQALVEENIISPM
          E.KDGAR.AA.ADKKKGLIG.LTELDTKDVDALLKKSEAQHEQPE..CPFGALTQRLLQALVEENIISPM
Retrocopy E-KDGARVAAMADKKKGLIGSLTELDTKDVDALLKKSEAQHEQPENRCPFGALTQRLLQALVEENIISPM

Parental  EDSPIPDMSGKESGADGASTSPRNQNKPFSVPHTKSLESRIKEELIAQGLLESEDRPAEDSEDEVLAELR
          EDSPIPDMSG.ESGADGASTS.RNQNKPFSVPHTKSLESRIKEELIAQ.LLESEDRP.EDSEDEV.A.LR
Retrocopy EDSPIPDMSGEESGADGASTSARNQNKPFSVPHTKSLESRIKEELIAQDLLESEDRPPEDSEDEVFAVLR

Parental  KRQAELKALSAHNRTKKHDLLRLAKEEVSRQELRQRVRMADNEVMDAFRKIMAARQKKRTPTKKEKDQAW
          KRQAELKALSAHNRTKKHDLLRL.KEEVSRQEL.QR.RMADNEVMDAFRKIMAA.QKKRTPTKKEKDQAW
Retrocopy KRQAELKALSAHNRTKKHDLLRLTKEEVSRQELSQRARMADNEVMDAFRKIMAAQQKKRTPTKKEKDQAW

Parental  KTLKERESIL
          KTLKER..IL
Retrocopy KTLKERKNIL

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_1479 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1479 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 ,