RetrogeneDB ID: retro_ocun_152

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:47821425..47821914(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027959
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000000248
• Aliases: None
• Description: None

Sequence

>retro_ocun_152
CGAGCGGAACTGGCCTCCGGCCGGATAGAACTCAACAAAAATCCAGTGGAAGGCTTTTCAGCAGGTTTAATAGATGACAA
TGATCTCTACCGATGGGAAGTCCTTATTATTGGTCCTCCAGATACACTATATGAAGGTGGTGTTTTTAAGGCTCACCTCA
CTTTTCCAAAGGATTATCCCCTCAGGCCTCCTAAAATGAAATTCATTACAGAAATCTGGCACCCAAATGTTGATAAAAAT
GGTGATGTTTGCATTTCTATTCTTCATGAGCCTGGGGAAGATAAATATGGTTATGAAAAGCCAGAGGAACGTTGGCTGCC
TATCCATACTGTGGAAACCATCATAAGTGTCATTTCTATGCTGGCAGACCCTAATGGAGACTCACCAGCTAATGTTGATG
CCGCGAAAGAATGGAGGGAAGACGGAAATGGAGAATTTAAAAGGAAAGTTGCCCGCTGTGTAAGAAAAAAGCCAAGAGAC
TGCTTTCGA

Alignment

ORF - retro_ocun_152 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 91.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELNKNPVEGFSAGLIDDNDLYRWEVLIIGPPDTLYEGGVFKAHLTFPKDYPLRPPKMKFITEIWHPNVDK
          ELNKNPVEGFSAGLIDDNDLYRWEVLIIGPPDTLYEGGVFKAHLTFPKDYPLRPPKMKFITEIWHPNVDK
Retrocopy ELNKNPVEGFSAGLIDDNDLYRWEVLIIGPPDTLYEGGVFKAHLTFPKDYPLRPPKMKFITEIWHPNVDK

Parental  NGDVCISILHEPGEDKYGYEKPEERWLPIHTVETIMISVISMLADPNGDSPANVDAAKEWREDRNGEFKR
          NGDVCISILHEPGEDKYGYEKPEERWLPIHTVETI.ISVISMLADPNGDSPANVDAAKEWRED.NGEFKR
Retrocopy NGDVCISILHEPGEDKYGYEKPEERWLPIHTVETI-ISVISMLADPNGDSPANVDAAKEWREDGNGEFKR

Parental  KVARCVRKSQETAF
          KVARCVRK.....F
Retrocopy KVARCVRKKPRDCF

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	1.88 RPM	13.36 RPM
SRP017611_kidney	2.13 RPM	9.22 RPM
SRP017611_liver	0.69 RPM	6.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_152 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_152 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014433	1 retrocopy	retro_btau_604,
Choloepus hoffmanni	ENSCHOG00000011801	1 retrocopy	retro_chof_2181,
Ciona savignyi	ENSCSAVG00000009498	1 retrocopy	retro_csav_4,
Macropus eugenii	ENSMEUG00000009769	3 retrocopies	retro_meug_360, retro_meug_473, retro_meug_647,
Myotis lucifugus	ENSMLUG00000002118	1 retrocopy	retro_mluc_104,
Oryctolagus cuniculus	ENSOCUG00000000248	1 retrocopy	retro_ocun_152 ,
Oryctolagus cuniculus	ENSOCUG00000023588	3 retrocopies	retro_ocun_131, retro_ocun_1719, retro_ocun_1793,
Otolemur garnettii	ENSOGAG00000008795	1 retrocopy	retro_ogar_2554,
Rattus norvegicus	ENSRNOG00000010041	3 retrocopies	retro_rnor_2496, retro_rnor_317, retro_rnor_970,
Sarcophilus harrisii	ENSSHAG00000002399	1 retrocopy	retro_shar_75,
Tupaia belangeri	ENSTBEG00000006117	1 retrocopy	retro_tbel_2852,
Tetraodon nigroviridis	ENSTNIG00000008566	1 retrocopy	retro_tnig_11,
Takifugu rubripes	ENSTRUG00000005995	1 retrocopy	retro_trub_4,
Tursiops truncatus	ENSTTRG00000000595	1 retrocopy	retro_ttru_1578,
Drosophila melanogaster	FBgn0058045	1 retrocopy	retro_dmel_6,