RetrogeneDB ID: retro_ocun_730

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:144454376..144454866(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TATDN1
• Ensembl ID: ENSOCUG00000017403
• Aliases: None
• Description: TatD DNase domain containing 1 [Source:HGNC Symbol;Acc:24220]

Sequence

>retro_ocun_730
TATTTTGAAAAATAATTTGAAGTGTCAGAACAAACAATATTGACAATGTTTCTTCATTGTCAAAACTCTCATGCTGAATT
TTTAGATATAATGATAGAAACAGGGAACAGTGTGTAGGTGAAATTGTGCATGCATTTGATGGGACCAGGGAGGCTGCAGC
TGCTCTGATTTGAGTTGGACCTTTACATAGGTTTTAGTGATTCCTCACTGAACCTTGAGGCTAATTTGGTAAGTTTGAAG
TCAATACCTAGTGAAAATTATTGATTTAGATGCATGTGCCTTGTTGTTGGAGTCAAAATTACATGTGCTAGATCAAAATT
TATAAATAACCTTATTTCACACCAAAAAGAAGTGGGAAAATGGGCATTGCATAAAAGATATAAATGAATCCTTCCATATA
GTTCAAATACTGGAGATAATGTCGGTTGTAAGAGATGAGAACCCAATGGAATTAGCCAATATGCTAGATAACAACGTCAT
TAAAATATTT

Alignment

ORF - retro_ocun_730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.24 %
• Parental protein coverage: 54.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YFEKQFELSERTKLPMFLHCRNSHAEFLDIM-KRNRDRCVGGVVHSFDGTKEAAAALI-DLDLYIGFNGC
          YFEK.FE.SE.T.L.MFLHC.NSHAEFLDIM..RNR..CVG..VH.FDGT.EAAAALI..LDLYIGF...
Retrocopy YFEK*FEVSEQTILTMFLHCQNSHAEFLDIM<DRNREQCVGEIVHAFDGTREAAAALI>ELDLYIGFSDS

Parental  SLKTEANLEVLKSIPTE-KLMIETDAPWC-GVKSTHAGSKFIK-TSFPTKKKWENGHCVKDRNEPCHIIQ
          SL..EANL..LKSIP.E.KL.I....P.C.GVK.T.A.SKFI..T.F.TKKKWENGHC.KD.NE..HI.Q
Retrocopy SLNLEANLVSLKSIPSE<KLLI*MHVPCC>GVKITCARSKFIN>TLFHTKKKWENGHCIKDINESFHIVQ

Parental  ILEIMSAVRDEDPLELANTLYNNTIKIF
          ILEIMS.VRDE.P.ELAN.L.NN.IKIF
Retrocopy ILEIMSVVRDENPMELANMLDNNVIKIF

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	18.87 RPM
SRP017611_kidney	0.00 RPM	17.74 RPM
SRP017611_liver	0.00 RPM	10.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_730 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_730 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_730 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033446	1 retrocopy	retro_btau_463,
Homo sapiens	ENSG00000147687	1 retrocopy	retro_hsap_578,
Gorilla gorilla	ENSGGOG00000015875	1 retrocopy	retro_ggor_514,
Nomascus leucogenys	ENSNLEG00000005467	1 retrocopy	retro_nleu_804,
Oryctolagus cuniculus	ENSOCUG00000017403	1 retrocopy	retro_ocun_730 ,
Rattus norvegicus	ENSRNOG00000047198	1 retrocopy	retro_rnor_1737,
Tupaia belangeri	ENSTBEG00000006179	1 retrocopy	retro_tbel_707,