RetrogeneDB ID: retro_ocun_204

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:34138630..34139473(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024649
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016136
• Aliases: None
• Description: None

Sequence

>retro_ocun_204
ATGGGAGAGATTAAAGTCTCTCCTGATTATAACTGGTTTAGAAGTACAGTTCCCCTTAAAAAGATTATCGTGGACGATGA
CGACAGTAAGATCTGGTCGCTGTATGATGCGGGCCCTCGGAGTATCAGGTGTCCTCTCATATTCCTCCCCCCTGTCAGCG
GGACTGCAGATGTGTTCTTCCGGCAAATTTTGGCTTTGACCGGATGGAGTTACCGGGTAATAGCTGTTCATCTTTTTGGG
GCTTCTTTGGGACGCTTTTTGGCCCAGAAATTTGCTGAATATACTCACAAGTCTCCCAGAGTCCATTCCCTCATCCTCTG
CAATGCCTTCAATGACACGTCTATCTTTAACCAGACTTGGACCGCAAACAGCTTTTGGCTGATGCCAGCATTTATGCTCA
AAAAAATAGTTCTTGGAAACTTTTCTTCTGGCCCAGTGGACCCTATGATGGCCAACGCCATTGACTTCATGGTGGACAGG
CTGGAAAGTTTGGGTCAGAGTGAACTGGCTTCCAGGCTTACCCTGAATTGTCAGAATTCTTACGTGGAACCTCATAAAAT
TCGGGACATCCCCGTGACCATCATGGATGTGTTTGATCAGAGTGCACTTTCAACCGAAGCGAAGGAGGAAATGTACAAAC
TGTATCCCAACGCCCGGAGAGCTCACCTTAAAACAGGAGGCAATTTCCCATACCTGTGCAGAAGTGCAGAGGTGAACCTT
TATGTACAGATACACTTGCTGCAGTTCCACGGAACCAAGTATGCGGCCATCGACCCGTCCATGGTCAGTGCCGAGGAGCT
CGAGGTGCAGAAGGGCAACCTCAGCCTCAGCCAGGAGGGAGCA

Alignment

ORF - retro_ocun_204 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.02 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHLFGASLGGFLAQKFAEYTHKSPRVHSLILCNAFSDTSIFNQTWTANSFWLMPAFMLKKIVLGNFSSGP
          VHLFGASLG.FLAQKFAEYTHKSPRVHSLILCNAF.DTSIFNQTWTANSFWLMPAFMLKKIVLGNFSSGP
Retrocopy VHLFGASLGRFLAQKFAEYTHKSPRVHSLILCNAFNDTSIFNQTWTANSFWLMPAFMLKKIVLGNFSSGP

Parental  VDPMMANAIDFMVDRLESLGQSELASRLTLNCQNSYVEPHKIRDIPVTIMDVFDQSALSTEAKEEMYKLY
          VDPMMANAIDFMVDRLESLGQSELASRLTLNCQNSYVEPHKIRDIPVTIMDVFDQSALSTEAKEEMYKLY
Retrocopy VDPMMANAIDFMVDRLESLGQSELASRLTLNCQNSYVEPHKIRDIPVTIMDVFDQSALSTEAKEEMYKLY

Parental  PNARRAHLKTGGNFPYLCRSAEVNLYVQIHLLQFHGTKYAAIDPSMVSAEELEVQKGNLSLSQE
          PNARRAHLKTGGNFPYLCRSAEVNLYVQIHLLQFHGTKYAAIDPSMVSAEELEVQKGNLSLSQE
Retrocopy PNARRAHLKTGGNFPYLCRSAEVNLYVQIHLLQFHGTKYAAIDPSMVSAEELEVQKGNLSLSQE

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	1.27 RPM	13.58 RPM
SRP017611_kidney	5.37 RPM	49.46 RPM
SRP017611_liver	2.00 RPM	32.45 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_204 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005282	1 retrocopy	retro_cjac_67,
Macropus eugenii	ENSMEUG00000013791	1 retrocopy	retro_meug_116,
Oryctolagus cuniculus	ENSOCUG00000016136	1 retrocopy	retro_ocun_204 ,
Otolemur garnettii	ENSOGAG00000010385	1 retrocopy	retro_ogar_3249,
Ictidomys tridecemlineatus	ENSSTOG00000010101	1 retrocopy	retro_itri_1397,