RetrogeneDB ID: retro_ocun_183

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018781:71019..71436(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000014416
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016739
• Aliases: None
• Description: None

Sequence

>retro_ocun_183
AGGTTGCAGGAGGATCCTCCAGCTGCAGTCAGCGGGGCTCCGTCTGAGAACAACATAATGGTTTGGAATGCGGTCATTTT
GGGGCCTGAGGGGACCCCATTTGAGGATGGAACATTCAAACTTACAATAGAATTCACTGAAGAATACCCAAACAAGCCAC
CCACAGTTAGATTTGTCTCTAAGATGTTTCATCCAAATGTCTATGCAGATGGTAGTATATGTCTAGACATACTTCAGAAC
CGCTGGAGTCCGACCTACGATGTATCTTCCATTTTAACATCCATACAGTCTCTATTGGATGAACCAAATCCCAATAGTCC
AGCAAACAGCCAGGCTGCTCAGCTGTACCAGGAGAACAAGCGGGAATATGAAAAACGTGTTTCTGCCATAGTAGAACAGA
GCTGGTGGGATTGTTGA

Alignment

ORF - retro_ocun_183 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.83 %
• Parental protein coverage: 63.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTVRFVSKMFHPNVYAD
          RLQEDPPA.VSGAPSENNIMVWNAVI.GPEGTPFEDGTFKLTIEFTEEYPNKPPTVRFVSKMFHPNVYAD
Retrocopy RLQEDPPAAVSGAPSENNIMVWNAVILGPEGTPFEDGTFKLTIEFTEEYPNKPPTVRFVSKMFHPNVYAD

Parental  GSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWRDC
          GSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSW.DC
Retrocopy GSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWWDC

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	50.39 RPM
SRP017611_kidney	0.00 RPM	38.92 RPM
SRP017611_liver	0.08 RPM	9.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_183 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_183 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001079	1 retrocopy	retro_chof_1316,
Callithrix jacchus	ENSCJAG00000005098	2 retrocopies	retro_cjac_1180, retro_cjac_3862,
Cavia porcellus	ENSCPOG00000011908	1 retrocopy	retro_cpor_489,
Dasypus novemcinctus	ENSDNOG00000007060	1 retrocopy	retro_dnov_215,
Macropus eugenii	ENSMEUG00000003026	1 retrocopy	retro_meug_2180,
Monodelphis domestica	ENSMODG00000010209	1 retrocopy	retro_mdom_341,
Oryctolagus cuniculus	ENSOCUG00000016739	1 retrocopy	retro_ocun_183 ,
Otolemur garnettii	ENSOGAG00000024335	1 retrocopy	retro_ogar_3203,
Procavia capensis	ENSPCAG00000005045	1 retrocopy	retro_pcap_222,
Sus scrofa	ENSSSCG00000012621	1 retrocopy	retro_sscr_29,
Tarsius syrichta	ENSTSYG00000000888	1 retrocopy	retro_tsyr_676,