RetrogeneDB ID: retro_ocun_47

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:72381513..72382272(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022236
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006100
• Aliases: None
• Description: None

Sequence

>retro_ocun_47
ATGGAAGGCGAGATGGAGACACAGGGTGCTGGGTCCGAGGACGGCTTCACTCAAGTCACTCGCAAGGGTGGCCGGCGGGC
GAAGAAACGGCAGGCTGAGCAGCTGTCCGCATCCGGGGAGGGCGGGGATGCGGGCCGCATGGACACCGAGGAGGCCCGGC
CGGCCAAGAGGCCCGTCTTCCCGCCCCTGTCCGGGGACGGACTCCTGGGTGGGAAAGAAGAAACGAGGAAGATTCCAGTC
CCAGCCAACAGGTACACCCCGCTGAAGGAAAACTGGATGAAGATATTCACTCCTATTGTAGAACACTTGGGCCTTCAGAT
TCGCTTTAACTTGAAATCAAGGAATGTGGAGATCAGGACTTGTAAAGAAACCAAGGATGTCAGTGCTCTGACCAAAGCTG
CTGATTTTGTGAAAGCCTTTCTTCTTGGCTTTCAGGTGGAGGATGCACTGGCTCTCATCAGATTGGATGACCTCTTCCTA
GAGTCTTTTGAAATAACTGATGTTAAGCCCCTAAAGGGAGACCACCTGTCTAGGGCAATCGGAAGAATTGCCGGCAAAGG
AGGAAAAACCAAATTCACCATAGAGAATGTGACACGGACACGGATAGTTTTGGCTGATGTGAAAGTTCACATCCTTGGCT
CTTTCCAAAACATCAAGATGGCGAGAACTGCCATTTGTAACCTCATCCTGGGAAATCCTCCCTCAAAGGTTTACGGCAAC
ATTCGAGCTGTGGCTAGCAGAGCAGCAGATCGATTCTGA

Alignment

ORF - retro_ocun_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MEGEMETQGAGSEDGFTQVTRKGGRRAKKRQAEQLSASGEGGDAGRMDTEEARPAKRPVFPPLSGDGLLG
          MEGEMETQGAGSEDGFTQVTRKGGRRAKKRQAEQLSASGEGGDAGRMDTEEARPAKRPVFPPLSGDGLLG
Retrocopy MEGEMETQGAGSEDGFTQVTRKGGRRAKKRQAEQLSASGEGGDAGRMDTEEARPAKRPVFPPLSGDGLLG

Parental  GKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAF
          GKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAF
Retrocopy GKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAF

Parental  LLGFQVEDALALIRLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKVH
          LLGFQVEDALALIRLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKVH
Retrocopy LLGFQVEDALALIRLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKVH

Parental  ILGSFQNIKMARTAICNLILGNPPSKVYGNIRAVASRAADRF
          ILGSFQNIKMARTAICNLILGNPPSKVYGNIRAVASRAADRF
Retrocopy ILGSFQNIKMARTAICNLILGNPPSKVYGNIRAVASRAADRF

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	3.31 RPM
SRP017611_kidney	0.00 RPM	4.76 RPM
SRP017611_liver	0.00 RPM	1.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_47 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_47 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_47 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003256	1 retrocopy	retro_cfam_1886,
Callithrix jacchus	ENSCJAG00000006564	3 retrocopies	retro_cjac_2615, retro_cjac_273, retro_cjac_4127,
Felis catus	ENSFCAG00000025330	2 retrocopies	retro_fcat_1521, retro_fcat_864,
Loxodonta africana	ENSLAFG00000000046	1 retrocopy	retro_lafr_419,
Microcebus murinus	ENSMICG00000010897	1 retrocopy	retro_mmur_516,
Myotis lucifugus	ENSMLUG00000010850	1 retrocopy	retro_mluc_1719,
Macaca mulatta	ENSMMUG00000017461	2 retrocopies	retro_mmul_102, retro_mmul_352,
Nomascus leucogenys	ENSNLEG00000009993	1 retrocopy	retro_nleu_2389,
Oryctolagus cuniculus	ENSOCUG00000006100	1 retrocopy	retro_ocun_47 ,
Otolemur garnettii	ENSOGAG00000016637	1 retrocopy	retro_ogar_3025,
Pongo abelii	ENSPPYG00000012353	1 retrocopy	retro_pabe_1232,
Rattus norvegicus	ENSRNOG00000005524	1 retrocopy	retro_rnor_712,
Sus scrofa	ENSSSCG00000008352	2 retrocopies	retro_sscr_114, retro_sscr_352,
Tarsius syrichta	ENSTSYG00000004007	1 retrocopy	retro_tsyr_1625,