RetrogeneDB ID: retro_ocun_1178

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:141022361..141022874(+)
• Located in intron of: ENSOCUG00000008539

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAWR
• Ensembl ID: ENSOCUG00000013722
• Aliases: None
• Description: PRKC, apoptosis, WT1, regulator [Source:HGNC Symbol;Acc:8614]

Sequence

>retro_ocun_1178
TCCTCCGAGTGCTTAGATGAGTATGACGACGATGAAGCAGGACAGAAGGAGCGGAGACGAGAAGATGCAGTCACACAACA
GAACACAATGCAGAATGAAGCTGTCAGCTTAGTAGACCCAGGCGGTTCCTATCTGCCACGGGAACCATCTAGAACAGTTT
CAGGCAGATACAAAAGTACAGCTGCTGCCTCTGAAGAAGATGGATCAAGTCGATATCCACGAACAGATAGGAGTGGGTTC
AGTAGATATAACAGGGATGGAAATGCTTCAGGTAATCTGCTATCTAGTAGTGCATTGGAAAAGAAAATTGAAGAACTTGA
AAAGGAAATACTAAGAGAAAGGCAAGAAAACCTAAGGCTTGTGAGACTGATGCAAGATAAAGAAGAAATGATTGGAAAAC
TCAAGGAAGAAATTGATATGTTAAATAGAGAACTGGATGACATAGAAGATGAAAATCAACAACTAAAGCAGGAAAATAAA
ACTCTTTTGAAAGTTGTTGGGCAGTTGACAAGG

Alignment

ORF - retro_ocun_1178 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.66 %
• Parental protein coverage: 50.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAECLDEYDDDEAGQKERRREDAVTQQNTMQNEAVSLVDPGGSYLPQEPSRTVSGRYKSTAAASEEDGSS
          ..ECLDEYDDDEAGQKERRREDAVTQQNTMQNEAVSLVDPGGSYLP.EPSRTVSGRYKSTAAASEEDGSS
Retrocopy SSECLDEYDDDEAGQKERRREDAVTQQNTMQNEAVSLVDPGGSYLPREPSRTVSGRYKSTAAASEEDGSS

Parental  RYPRTDRSGFSRYNRDGNASGNLLSSSALEKKIEELEKEILRERQENLRLVRLMQDKEEMIGKLKEEIDM
          RYPRTDRSGFSRYNRDGNASGNLLSSSALEKKIEELEKEILRERQENLRLVRLMQDKEEMIGKLKEEIDM
Retrocopy RYPRTDRSGFSRYNRDGNASGNLLSSSALEKKIEELEKEILRERQENLRLVRLMQDKEEMIGKLKEEIDM

Parental  LNRELDDVEDENQQLKQENKTLLKVVGQLTR
          LNRELDD.EDENQQLKQENKTLLKVVGQLTR
Retrocopy LNRELDDIEDENQQLKQENKTLLKVVGQLTR

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	0.06 RPM	0.99 RPM
SRP017611_kidney	0.61 RPM	5.47 RPM
SRP017611_liver	0.54 RPM	2.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1178 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1178 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	ENSOCUG00000013722	1 retrocopy	retro_ocun_1178 ,