RetrogeneDB ID: retro_ocun_39

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:4571963..4572602(-)
• Located in intron of: ENSOCUG00000008236

Retrocopy information

• Ensembl ID: ENSOCUG00000025915
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000009302
• Aliases: None
• Description: None

Sequence

>retro_ocun_39
ATGAGCGGAACCCTGGGAAAGGTGCTGTGCCTGAGGAGCAATATCATTTTTAAGCAAGTGGTTTCCCTCTTAAGAGTCAG
AACTTCAGGAGAGAATCCCATTTATTCTGCAGGTGGCATTCTACTGAGCACCAGTCGGCACTACAAGTCAAAACCCACCC
ATGGCATTGGACGATACAAGCACCTAATTAAAGCTCAGGAGCCCAAGAAGAAGAGGGGAAAAGTAGAAGTGAGACCCATC
AATTTGGGGACAGATTATGAATATGGGGTTTTAAACGTTCACCTCACTGCCTACGACATGACCCTGGCAGAGAGTTACGC
CCGATACATTCACAACCTCTGCAACCAGCTTTCCATTAAAGTTGAAGAAAGTTACGCGATGCCCACCAAAACCATGGAGG
TGTTGCAGCTGCAGGATCAAGGCACCAAAATGTTCGTGGACTCAGTCCTTACCACACACGAGCGAGTGGTTCAGATCAGC
GGTTTGAGTGCTACATTTGCAGAGATTTTCTTGGAAATAATCCAGAGTAATCTTCCTGAAGGAGTCAGACTGTCAGTGAG
GGAGCACACCGAAGAAGACTTCAAAGGACGGTTCAAAGCCCGGCCTGAACTAGAAGAACTATTGGCCAAACTGAACTAG

Alignment

ORF - retro_ocun_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGILLSTSRHYKSKPTHGIGRYKHLIKAQEPKKKRGKVEVRPINLGTDYEYGVLNVHLTAYDMTLAESYA
          GGILLSTSRHYKSKPTHGIGRYKHLIKAQEPKKKRGKVEVRPINLGTDYEYGVLNVHLTAYDMTLAESYA
Retrocopy GGILLSTSRHYKSKPTHGIGRYKHLIKAQEPKKKRGKVEVRPINLGTDYEYGVLNVHLTAYDMTLAESYA

Parental  RYIHNLCNQLSIKVEESYAMPTKTMEVLQLQDQGTKMFVDSVLTTHERVVQISGLSATFAEIFLEIIQSN
          RYIHNLCNQLSIKVEESYAMPTKTMEVLQLQDQGTKMFVDSVLTTHERVVQISGLSATFAEIFLEIIQSN
Retrocopy RYIHNLCNQLSIKVEESYAMPTKTMEVLQLQDQGTKMFVDSVLTTHERVVQISGLSATFAEIFLEIIQSN

Parental  LPEGVRLSVREHTEEDFKGRFKARPELEELLAKLN
          LPEGVRLSVREHTEEDFKGRFKARPELEELLAKLN
Retrocopy LPEGVRLSVREHTEEDFKGRFKARPELEELLAKLN

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	3.92 RPM	8.28 RPM
SRP017611_kidney	6.18 RPM	12.37 RPM
SRP017611_liver	1.77 RPM	4.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_39 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_39 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_39 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005585	1 retrocopy	retro_cfam_1437,
Choloepus hoffmanni	ENSCHOG00000003662	1 retrocopy	retro_chof_2664,
Homo sapiens	ENSG00000175581	1 retrocopy	retro_hsap_3557,
Mustela putorius furo	ENSMPUG00000009716	1 retrocopy	retro_mputfur_38,
Mus musculus	ENSMUSG00000030706	2 retrocopies	retro_mmus_2478, retro_mmus_563,
Nomascus leucogenys	ENSNLEG00000017097	1 retrocopy	retro_nleu_1376,
Oryctolagus cuniculus	ENSOCUG00000009302	1 retrocopy	retro_ocun_39 ,
Otolemur garnettii	ENSOGAG00000004771	1 retrocopy	retro_ogar_234,
Pan troglodytes	ENSPTRG00000004049	1 retrocopy	retro_ptro_2417,
Tursiops truncatus	ENSTTRG00000005403	2 retrocopies	retro_ttru_1123, retro_ttru_297,
Vicugna pacos	ENSVPAG00000004657	1 retrocopy	retro_vpac_538,