RetrogeneDB ID: retro_ocun_170

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:20505115..20505694(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025017
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000004238
• Aliases: None
• Description: None

Sequence

>retro_ocun_170
ATGCTGCGCTGCGGCCTGGCCTGCGAACGCTGCAGGTGGATCCTGCCCCTGCTCCTGCTCAGCGCCATCGCCTTCGACAT
CATAGCGCTGGCCGGCCGCGGCTGGCTGCAGTCGAACGACCATGGCCAGACGTCCTCGCTCTGGTGGAAATGCCTGGGCG
AGGGCGGCGGCAGCGGGTCCTACGAGGAAGGATGCCAGAGCCTCATGGAGTACGCGTGGGGACGGGCGGCGGCCGCCATG
CTCTTCTGCGGATTTATCATCCTCGTCATCTGCTTCGTGCTGTCCTTCTTCGCCCTCTGCGGACCCCAGATGCTGGTCTT
CCTCAGAGTGATCGGGGGCCTTCTCGCCCTGGCTGCTGTGTTCCAGATCATCTCGCTGGTAATTTACCCAGTCAAGTACA
CCCAGACCTTCAACCTTCATCTCAACCCTGCTGTCACGTACATCTTTAACTGGGCCTATGGCTTTGGGTGGGCAGCCACG
ATCATCCTGATTGGCTGTGCCTTCTTCTTCTGCTGTCTCCCCAACTACGAGGATGACCTGCTGGGCAATGCGAAGCCCAG
GTACTTCTACACCTCGGCC

Alignment

ORF - retro_ocun_170 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRCGLACERCRWILPLLLLSAIAFDIIALAGRGWLQSSDHGQTSSLWWKCLGEGGGSGSYEEGCQSLME
          MLRCGLACERCRWILPLLLLSAIAFDIIALAGRGWLQS.DHGQTSSLWWKCLGEGGGSGSYEEGCQSLME
Retrocopy MLRCGLACERCRWILPLLLLSAIAFDIIALAGRGWLQSNDHGQTSSLWWKCLGEGGGSGSYEEGCQSLME

Parental  YAWGRAAAAMLFCGFIILVICFVLSFFALCGPQMLVFLRVIGGLLALAAVFQIISLVIYPVKYTQTFNLH
          YAWGRAAAAMLFCGFIILVICFVLSFFALCGPQMLVFLRVIGGLLALAAVFQIISLVIYPVKYTQTFNLH
Retrocopy YAWGRAAAAMLFCGFIILVICFVLSFFALCGPQMLVFLRVIGGLLALAAVFQIISLVIYPVKYTQTFNLH

Parental  LNPAVTYIFNWAYGFGWAATIILIGCAFFFCCLPNYEDDLLGNAKPRYFYTSA
          LNPAVTYIFNWAYGFGWAATIILIGCAFFFCCLPNYEDDLLGNAKPRYFYTSA
Retrocopy LNPAVTYIFNWAYGFGWAATIILIGCAFFFCCLPNYEDDLLGNAKPRYFYTSA

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	0.99 RPM
SRP017611_kidney	0.00 RPM	32.33 RPM
SRP017611_liver	0.08 RPM	29.13 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_170 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_170 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020097	1 retrocopy	retro_btau_165,
Callithrix jacchus	ENSCJAG00000019024	1 retrocopy	retro_cjac_3992,
Homo sapiens	ENSG00000112378	2 retrocopies	retro_hsap_1523, retro_hsap_2901,
Gorilla gorilla	ENSGGOG00000028340	1 retrocopy	retro_ggor_1165,
Macropus eugenii	ENSMEUG00000004872	1 retrocopy	retro_meug_845,
Microcebus murinus	ENSMICG00000013979	1 retrocopy	retro_mmur_353,
Myotis lucifugus	ENSMLUG00000001473	1 retrocopy	retro_mluc_2287,
Macaca mulatta	ENSMMUG00000000997	1 retrocopy	retro_mmul_2156,
Nomascus leucogenys	ENSNLEG00000014930	2 retrocopies	retro_nleu_1934, retro_nleu_631,
Oryctolagus cuniculus	ENSOCUG00000004238	1 retrocopy	retro_ocun_170 ,
Otolemur garnettii	ENSOGAG00000011669	1 retrocopy	retro_ogar_631,
Pongo abelii	ENSPPYG00000017043	3 retrocopies	retro_pabe_1267, retro_pabe_2400, retro_pabe_2416,