RetrogeneDB ID: retro_ocun_1721

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018818:261265..261564(+)
• Located in intron of: ENSOCUG00000008015

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM208
• Ensembl ID: ENSOCUG00000026215
• Aliases: None
• Description: transmembrane protein 208 [Source:HGNC Symbol;Acc:25015]

Sequence

>retro_ocun_1721
ATGGCACCCAAGGGCAGAGTGGGCATGGGAGGAAGAAACAGATCTTTGAAGAGAATGGAGAGCCCTGAGTTCCACCTGTG
CACCATCCTGGGGCCAACACCATCACTGCCTGTGACCTTAGTCTCCTTCTACTCAGTGGCTTTGTTTGGGGCCGTGATGG
CCCTGGGCTTCAGTCTGGCAGTGTGTGGGGCCAGCAGCCGCTCTCTGAGCTCCTGGCCTGGGCAGCCTTCTCCAAGGATG
GGGGCTTGGTGGGTGGGGCGGGGATCTCATGCGGAGCAGGGCATGCAGAGCACCTCAGG

Alignment

ORF - retro_ocun_1721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.27 %
• Parental protein coverage: 59.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LQPKGKVGTRGKKQIFEENRETLKFYLRIILG-ANAI-YCL-VTLVFFYSSASFWAWMALGFSLAVYGAS
          ..PKG.VG..G.........E...F.L..ILG.AN.I..CL.VTLV.FYS.A.F.A.MALGFSLAV.GAS
Retrocopy MAPKGRVGMGGRNRSLKR-MESPEFHLCTILG<ANTI<HCL<VTLVSFYSVALFGAVMALGFSLAVCGAS

Parental  YHSMSS-MARAAFSEDGALMDGGMDLNMEQGMAEHLK
          ..S.SS..A.AAFS.DG.L..GG.......G.AEHL.
Retrocopy SRSLSS<LAWAAFSKDGGLV-GGAGISCGAGHAEHLR

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	17.66 RPM
SRP017611_kidney	0.10 RPM	35.17 RPM
SRP017611_liver	0.00 RPM	9.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1721 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1721 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000026215	2 retrocopies	retro_ocun_1721 , retro_ocun_1722,
Ochotona princeps	ENSOPRG00000002571	2 retrocopies	retro_opri_944, retro_opri_959,
Sus scrofa	ENSSSCG00000002790	1 retrocopy	retro_sscr_273,