RetrogeneDB ID: retro_ocun_151

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:104784724..104785186(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000016091
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016057
• Aliases: None
• Description: None

Sequence

>retro_ocun_151
ATGACCAAAATAAAGTCTGACCCCGACGGGCCCGAGGCCCAGGGAGAGGCGTGCGGCGGGGAGCGCACCTATCAGGAGCT
GCTGGTCAACCTGAACCCCATCGCGCAGCCCCTGGCTTTGCGCCGCCTCACGCGGAAGCTCTACAAGTGCATCAAGAAAG
CCGTGAAGCAGAAGCAGATCCGGCGCGGGGTGAAGGAGGTTCAGAAGTTTGTCAACAAGGGCGAGAAAGGGATCATGGTT
CTGGCAGGAGACACACTGCCCATTGAAGTATACTGCCACCTCCCAGTTATGTGTGAGGACCGGAATCTGCCCTACGTCTA
CATCCCCTCGAAGACAGATCTGGGTGCAGCTGCGGGCTCCAAGCGCCCCACCTGTGTGATTATGGTTAAGCCTCACGAGG
AATACCAGGAGGCCTACGATGAGTGCCTGGAGGAGGTGCAGGCCCTGCCCTCACCCCACTGA

Alignment

ORF - retro_ocun_151 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTKIKSDPDGPEAQGEACGGERTYHELLVNLNPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQKF
          MTKIKSDPDGPEAQGEACGGERTY.ELLVNLNPIAQPLA.RRLTRKLYKCIKKAVKQKQIRRGVKEVQKF
Retrocopy MTKIKSDPDGPEAQGEACGGERTYQELLVNLNPIAQPLALRRLTRKLYKCIKKAVKQKQIRRGVKEVQKF

Parental  VNKGEKGIMVLAGDTLPIEVYCHLPVMCEDRNLPYVYIPSKTDLGAAAGSKRPTCVIMVKPHEEYQEAYD
          VNKGEKGIMVLAGDTLPIEVYCHLPVMCEDRNLPYVYIPSKTDLGAAAGSKRPTCVIMVKPHEEYQEAYD
Retrocopy VNKGEKGIMVLAGDTLPIEVYCHLPVMCEDRNLPYVYIPSKTDLGAAAGSKRPTCVIMVKPHEEYQEAYD

Parental  ECLEEVQALPSPH
          ECLEEVQALPSPH
Retrocopy ECLEEVQALPSPH

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	9.99 RPM
SRP017611_kidney	0.10 RPM	17.23 RPM
SRP017611_liver	0.00 RPM	7.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_151 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_151 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012244	1 retrocopy	retro_cjac_264,
Homo sapiens	ENSG00000145912	2 retrocopies	retro_hsap_3712, retro_hsap_611,
Gorilla gorilla	ENSGGOG00000000015	1 retrocopy	retro_ggor_2509,
Macropus eugenii	ENSMEUG00000003839	2 retrocopies	retro_meug_285, retro_meug_320,
Macaca mulatta	ENSMMUG00000018757	1 retrocopy	retro_mmul_1702,
Monodelphis domestica	ENSMODG00000004231	1 retrocopy	retro_mdom_345,
Mus musculus	ENSMUSG00000001056	1 retrocopy	retro_mmus_565,
Oryctolagus cuniculus	ENSOCUG00000016057	1 retrocopy	retro_ocun_151 ,
Ochotona princeps	ENSOPRG00000007907	3 retrocopies	retro_opri_305, retro_opri_421, retro_opri_810,
Pongo abelii	ENSPPYG00000016105	3 retrocopies	retro_pabe_1704, retro_pabe_3143, retro_pabe_481,
Rattus norvegicus	ENSRNOG00000004247	2 retrocopies	retro_rnor_1436, retro_rnor_2198,
Sus scrofa	ENSSSCG00000014032	1 retrocopy	retro_sscr_407,