RetrogeneDB ID: retro_ocun_1055

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:97277769..97278183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM3D
• Ensembl ID: ENSOCUG00000002770
• Aliases: None
• Description: family with sequence similarity 3, member D [Source:HGNC Symbol;Acc:18665]

Sequence

>retro_ocun_1055
GAGGGTAGCAGTTTAATGAGCGGCGTGAAGAACAACGTTGGAAGAGGGATCAACGTTGCCTTGGCAAATGGAAAAACAGG
AGAAGTATTAGACACTAAATATTTTGACATGTGGGGAGGAGATGTGGAACCGTTTATTGAGTTTCTTAAGGCCATACAAG
ATGGAACAATAGTTTTAATGGGAACATACGATGATGGAGCAACCAAACTCAATGATGAGGCACGGCGGCTCATTGCAGAA
TTGGGAAGTACATCTATTACTAATCTTGGTTTTAGAGACAACTGGGTCTTCTGTGGTGGGAAGGGCATTAAGACAAAAAG
CCCTTTTGAACAGCACATAAAGAACAATAAGGATACAAACAAATATGAAGGCTGGCCTGAAGTTGTAGAGATGGAAGGAT
GCATCCCCCAGAAG

Alignment

ORF - retro_ocun_1055 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.52 %
• Parental protein coverage: 61.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENHIIMSPVKNNVGRGLNIALVNGTTGLVLRHNSFDMYSGDPKSVLQFLKEVPMGTLVLVASYDDPGTKM
          E....MS.VKNNVGRG.N.AL.NG.TG.VL....FDM..GD......FLK....GT.VL...YDD..TK.
Retrocopy EGSSLMSGVKNNVGRGINVALANGKTGEVLDTKYFDMWGGDVEPFIEFLKAIQDGTIVLMGTYDDGATKL

Parental  NDDIRKLLSDLGSSYAKELGFRDSWVFLGARELKSKSPFEEYLKNNPDTNKYEGWPELLELEGCVPKK
          ND..R.L...LGS.....LGFRD.WVF.G....K.KSPFE...KNN.DTNKYEGWPE..E.EGC.P.K
Retrocopy NDEARRLIAELGSTSITNLGFRDNWVFCGGKGIKTKSPFEQHIKNNKDTNKYEGWPEVVEMEGCIPQK

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	17.55 RPM	0.11 RPM
SRP017611_kidney	8.82 RPM	28.38 RPM
SRP017611_liver	5.40 RPM	0.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1055 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000002770	3 retrocopies	retro_ocun_1055 , retro_ocun_1815, retro_ocun_1844,