RetrogeneDB ID: retro_ocun_275

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:18639492..18640066(+)
• Located in intron of: ENSOCUG00000011954

Retrocopy information

• Ensembl ID: ENSOCUG00000026284
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000015551
• Aliases: None
• Description: None

Sequence

>retro_ocun_275
ATGTTCCAGGGTGCAGAGAGTGAGGCTGGACGAGCAAGCTCCAGGGCCATGAAGTCCCCAGGAGGAGAATCCAGAAATCT
TTTCGGAAGTGCGGAAGAAGCCGTTCCTTTGAGCAGAACTAACAGGATGGCGTCTAATATTTTTGGACCAACTGAAGAAC
CTCAGCACCTGCCCAAGAGGACCAACCCCCCAGGGGCCAAAGGAAGTGGCATCTTCGAGGAGCTGACCCCTGTGCAGGCT
CGGCAGCGCCTGAACTCGCCGGGTGGGAAGACCAGTGACATTTTTGGGTCTCCGGTCACTACCACTTTTGTCCTCGGCAC
ATCCGAACAAACCCAAGGACCACATCCTCCTCCGAGAAGGAGAAGACCCGAGCCTGGACCCGAGAGCTGCAGCGGGAACC
CCATCCAGGGACGCGCCACTGGACGAGAGAGGCCGCTCCCGAGAAGCTAACCATGCCAAGGAGCCCGAACCCGCACCCCA
GGTCGACAGCCACGAGCCCAGGCTGGGGCCACGGCCTCGCTCCCACAACAAGATCCTGAACCCGCCAGGAGGCAAATCCA
GCATCTCCTTCTAC

Alignment

ORF - retro_ocun_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFHAAESEAGRASSRAMKPPGGESSNLFGSAEEAVPSSRPNRMASNIFGPTEEPQHLPKRTNPPGGKGSG
          MF..AESEAGRASSRAMK.PGGES.NLFGSAEEAVP.SR.NRMASNIFGPTEEPQHLPKRTNPPG.KGSG
Retrocopy MFQGAESEAGRASSRAMKSPGGESRNLFGSAEEAVPLSRTNRMASNIFGPTEEPQHLPKRTNPPGAKGSG

Parental  IFEELLSVQARQRLTRPGGKTSDIFG-VSGIVFIAP-NAHPRKTVDHILLREGEDPSLDPRAAAGTPSRD
          IFEEL..VQARQRL..PGGKTSDIFG.VSG.....P..AHP.K..DHILLREGEDPSLDPRAAAGTPSRD
Retrocopy IFEELTPVQARQRLNSPGGKTSDIFG<VSGHYHFCP<SAHPNKPKDHILLREGEDPSLDPRAAAGTPSRD

Parental  APLEEKGRSREANHAKEPEPTPQVDSHEPRLGPRPRSHNKVLNPPGGKSSISFY
          APL.E.GRSREANHAKEPEP.PQVDSHEPRLGPRPRSHNK.LNPPGGKSSISFY
Retrocopy APLDERGRSREANHAKEPEPAPQVDSHEPRLGPRPRSHNKILNPPGGKSSISFY

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	1.05 RPM	4.64 RPM
SRP017611_kidney	2.03 RPM	7.91 RPM
SRP017611_liver	0.54 RPM	3.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_275 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_275 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008232	1 retrocopy	retro_amel_1019,
Cavia porcellus	ENSCPOG00000005352	2 retrocopies	retro_cpor_749, retro_cpor_892,
Dipodomys ordii	ENSDORG00000007521	1 retrocopy	retro_dord_269,
Macropus eugenii	ENSMEUG00000008873	4 retrocopies	retro_meug_1471, retro_meug_1628, retro_meug_189, retro_meug_258,
Mus musculus	ENSMUSG00000024165	3 retrocopies	retro_mmus_1204, retro_mmus_655, retro_mmus_709,
Oryctolagus cuniculus	ENSOCUG00000015551	1 retrocopy	retro_ocun_275 ,
Pteropus vampyrus	ENSPVAG00000016673	1 retrocopy	retro_pvam_99,
Rattus norvegicus	ENSRNOG00000024661	2 retrocopies	retro_rnor_25, retro_rnor_560,
Sorex araneus	ENSSARG00000012440	1 retrocopy	retro_sara_335,
Sarcophilus harrisii	ENSSHAG00000012700	1 retrocopy	retro_shar_184,
Tursiops truncatus	ENSTTRG00000011377	1 retrocopy	retro_ttru_429,