RetrogeneDB ID: retro_rnor_546

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:259779371..259780218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dedd
• Ensembl ID: ENSRNOG00000003779
• Aliases: Dedd, Deft
• Description: Death effector domain-containing protein [Source:UniProtKB/Swiss-Prot;Acc:Q9Z2K0]

Sequence

>retro_rnor_546
ATGGCGGGCCTAAAGAATCGGGCAAGCCAGGTGTGGCCCGAAGAGCGTGTTGAGCAGGAACATGAGATCTACAGCCTCCA
CCGCATGTTTGACATCGTGGGCACCCACCTAACACACAGAGATGTTCGCGTGCGTTCCTTCCATTTTGTTGATGTTATTG
ACGACCATGAACGTGGACTCATCTGAAATGGACGTGACTTCTTATGGGCACTGGAGCGCCAGGGCCGCTGTGACGAGAGT
AACTTTCGTCAGGTGCTGTACCTATGACGCATCATCACTCGCCATGACCTGCTGCCCTACGTTTCTCCCAAGAAGAAACG
GGCTGTGTGCCCTGATCTCGTAGACAAGTATCTGGAGGAAACATCAATTCGCTATGTGATCCCCAGAGCCCTCAGTGATC
CAGAACCGAGGCCTCCCCAGCCCTTTAAAACAGTGCCTCCCCACTCACTATTCTGTGGTGTGCTGACCCACTTCGGGTCC
TCAAATGTGTAGTAAGCTGCCAGCCTGAGGGAGACCCACACTTGGGAGTCAGCGAAAACGACAGAAGTCAGTGACTCTAG
ACCTGAAGAAAAGGCAGACATGTGACATCAGGCTGTGAGTTCGAGCAGAATACTGCCAGCATGAGACTGCTCTGCAAGGC
ACTGTCTTCTCTAATAAGCAGGACCCACTTGAGCGCCAGTTTGAGCTTTTTAACCAGGCCAACACTATCCTCGAGTCCTG
GGACCTGGGCTCCATCATCTGTGACATCAAGTTCTCTGAGCTCACCTTCCTTAACGCATGGCGAGACTACATTAATGGAT
CATTATTAGAGGCACTGAAAGGCGTCTTCATCACAGACTCAAGCAAG

Alignment

ORF - retro_rnor_546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 88.68 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGLKRRASQVWPEERVEQEHGLYSLHRMFDIVGTHLTHRDVRVLSFLFVDVIDDHERGLIRNGRDFLLA
          MAGLK.RASQVWPEERVEQEH..YSLHRMFDIVGTHLTHRDVRV.SF.FVDVIDDHERGLI.NGRDFL.A
Retrocopy MAGLKNRASQVWPEERVEQEHEIYSLHRMFDIVGTHLTHRDVRVRSFHFVDVIDDHERGLI*NGRDFLWA

Parental  LERQGRCDESNFRQVLQLLRIITRHDLLPYVTLKKRRAVCPDLVDKYLEETSIRYVTPRALSDPEPRPPQ
          LERQGRCDESNFRQVL.L.RIITRHDLLPYV..KK.RAVCPDLVDKYLEETSIRYV.PRALSDPEPRPPQ
Retrocopy LERQGRCDESNFRQVLYL*RIITRHDLLPYVSPKKKRAVCPDLVDKYLEETSIRYVIPRALSDPEPRPPQ

Parental  PSKTVPPH-YPVVCC-PTSGSQMCSKRPARGRTTLGSQRKRRKSVTPDPKEKQTCDIRLRVRAEYCQHET
          P.KTVPPH....V.C.PTSG.QMCSK.PA.GR.TLGSQRKR.KSVT.D.K..QTCDIRL.VRAEYCQHET
Retrocopy PFKTVPPH>HYSVVC*PTSGPQMCSKLPA*GRPTLGSQRKRQKSVTLDLKKRQTCDIRL*VRAEYCQHET

Parental  ALQGNVFSNKQDPLERQFERFNQANTILKSRDLGSIICDIKFSELTYLDAFWRDYINGSLLEALKGVFIT
          ALQG.VFSNKQDPLERQFE.FNQANTIL.S.DLGSIICDIKFSELT.L.A.WRDYINGSLLEALKGVFIT
Retrocopy ALQGTVFSNKQDPLERQFELFNQANTILESWDLGSIICDIKFSELTFLNA-WRDYINGSLLEALKGVFIT

Parental  DSLK
          DS.K
Retrocopy DSSK

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	15.39 RPM
SRP017611_kidney	0.00 RPM	23.24 RPM
SRP017611_liver	0.00 RPM	14.79 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_546 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_546 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000013973	1 retrocopy	retro_mmus_2223,
Oryctolagus cuniculus	ENSOCUG00000002387	1 retrocopy	retro_ocun_1512,
Rattus norvegicus	ENSRNOG00000003779	1 retrocopy	retro_rnor_546 ,