RetrogeneDB ID: retro_ocun_504

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:50615989..50616732(+)
• Located in intron of: ENSOCUG00000015539

Retrocopy information

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

Parental gene information

• Parental gene symbol: TATDN3
• Ensembl ID: ENSOCUG00000004792
• Aliases: None
• Description: TatD DNase domain containing 3 [Source:HGNC Symbol;Acc:27010]

Sequence

>retro_ocun_504
GATGTGTTGGAGGAAGCCAAGAAGGGCAACGTTATGGCCCTTATGGCAGTTGCTGAACATTCAGGAGAATTTGAAAAGAT
TATGCAACTTTCAGAAAGGTATAATGGGCTTGTCCTGCCATGTTTGGGTGTTCACCCAGTCCAAGAACTACCATCAGAAG
ATCAGAGGAGTGTCACATCGAAGGATTTGGAAGTGGCTTTGCCTATTATTGGGCATTATAAGGATCAGTTATTGGCAATT
GGAGAAGTTGGACTAGATTTCACCCCCAGATTTGCTGGCACTGATGAACAGAAGGAAGAGCAAAGACAAGTCCTAATCAA
ACAAGTCCAATTAGCCAAAAGACTAAATTTGCCTTTAAATGTTCATTCCCGTTCAGCTGGAAGACCTTCCATCAACCTCT
TACATGAGCAAGGTGCTGTCAAAGTACTGCTGCACGGATCTGATGATCGGCCATCTGTAGCCATGAAGGAGTAAGAGCTG
GGTACTTCTTCTCCATACCCACTTCTGTCGTAAATGGACAGAAGCAGAAACTTGTAAAACAGTTGCCTTTATCTTCTATA
TGCTTAGAAACAGATTTGCCTGCACTAGGACCAGTACAACAAGTGCGAAATGAGCTCAGGAACATTTCCATTTCAGCAGA
ACATATTGTCTAAGTGAAAGGGATCTCAGTGGAAGAAGTTATAGAAGTGACAACACAGAACACATTGGAATGGTTTCCCA
AGCGTCAACACCTGCTGCAGAAA

Alignment

ORF - retro_ocun_504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86. %
• Parental protein coverage: 90.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DVLEEAKKVNVMALVAVAEHSREFEKIMQLSERYNGFVLPCLGVHPVQELPSEDQRSVTLKDLEVALPII
          DVLEEAKK.NVMAL.AVAEHS.EFEKIMQLSERYNG.VLPCLGVHPVQELPSEDQRSVT.KDLEVALPII
Retrocopy DVLEEAKKGNVMALMAVAEHSGEFEKIMQLSERYNGLVLPCLGVHPVQELPSEDQRSVTSKDLEVALPII

Parental  ERYKDRLLAIGEVGLDFTPRFAGTDEQKEEQRQVLIKQVQLAKRLNLPLNVHSRSAGRPTVSLLREQGAD
          ..YKD.LLAIGEVGLDFTPRFAGTDEQKEEQRQVLIKQVQLAKRLNLPLNVHSRSAGRP...LL.EQGA.
Retrocopy GHYKDQLLAIGEVGLDFTPRFAGTDEQKEEQRQVLIKQVQLAKRLNLPLNVHSRSAGRPSINLLHEQGAV

Parental  KVLLHAFDGRPSVAM-EGVRAGYFFSIPPSIIRSGQKQKLVKQLPLTSICLETDSPALGPVKQVRNEPRN
          KVLLH..D.RPSVAM.EGVRAGYFFSIP.S....GQKQKLVKQLPL.SICLETD.PALGPV.QVRNE.RN
Retrocopy KVLLHGSDDRPSVAM<EGVRAGYFFSIPTSVV-NGQKQKLVKQLPLSSICLETDLPALGPVQQVRNELRN

Parental  ISISAEYIAQVKGISVEEVIEVTTQNAMKLFPKLQHLLKK
          ISISAE.I..VKGISVEEVIEVTTQN....FPK.QHLL.K
Retrocopy ISISAEHIV*VKGISVEEVIEVTTQNTLEWFPKRQHLLQK

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	6.79 RPM
SRP017611_kidney	0.00 RPM	7.91 RPM
SRP017611_liver	0.00 RPM	7.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_504 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_504 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000004792	1 retrocopy	retro_ocun_504 ,