RetrogeneDB ID: retro_ocun_1634

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018731:234782..235877(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025576
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATAD1
• Ensembl ID: ENSOCUG00000012082
• Aliases: None
• Description: ATPase family, AAA domain containing 1 [Source:HGNC Symbol;Acc:25903]

Sequence

>retro_ocun_1634
TTAACAATCAAGATGGTACATGCTGAAGCCTTTTCTCGTCCCTTGAGTCGGAATGAAGTTGTCGGTTTAATTTTCCGTTT
GATGATATTTGGTGCAGTAACATACTTTACTATCAAATGGATGGTAGATGCAATTGATCCAACAAGAAAGCAAAAAGTAG
AAGCTCAGAAACAGGCAGAAAAATTGATGAAGCAAATTGGTGTGAAAAATGTGAAGCTTTCAGAATACGAAATGAGCATT
GCTGCTCATCTAGTAGACCCTCTTAACATGCATGTTACTTGGAGTGATATAGCAGGTTTAGATGATGTCATTACGGATCT
GAAGGACACAGTGATCTTACCTATCAAAAAGAAGCATTTGTTTGAGAATTCTAGACTTCTACAACCTCCAAAGGGTGTGC
TTCTCTATGGGCCTCCAGGCTGTGGTAAAACATTGATTGCTAAGGCGACAGCCAAAGAAGCAGGCTGCTGATTTATTAAC
CTTCAGCCTTCAACACTGACTGATAAGTGGTATGGAGAATCTCAGAAGTTGGCTGCTGCTGTTTTTTCTCTTGCCATAAA
GCTACAACCATCCATCATCTTTATAGATGAAATAGACTCCTTTCTAAGAAACCGTTCAAGTTCTGACCATGAAGCTACAG
CCATGATGAAAGCTCAGTTTATGAGTCTGTGGGATGGATTGGATACTGATCACAGCTGCCAGGTCATAGTGATGGGAGCT
ACTAATCGCCCTCAGGATCTTGACTCGGCTATAATGAGAAGAATGCCTACAAGATTTCATATCAACCAGCCTGCTCTAAA
ACAAAGAGAAGCAATTCTGAAGCTTATCTTGAAAAATGAAAATGTGGATAGGCATGTAGACCTGTTAGAAGTTGCCCAGG
AAACTGATGGTTTTTCAGGAAGTGACCTAAAAGAGATGTGTAGGGATGCTGCCCTCCTCTGTGTCAGGGAATATGTTAAT
TCCACATCAGAAGAAAGCCATGATGAAGATGAAATTCGGCCTGTGCAGCAGCAGGACCTACATCGGGCAATTGAAAAGAT
GAAGAAATCAAAGGATGCAGCATTTCAGAATGTTTTAACACATGTTTGTTTAGAT

Alignment

ORF - retro_ocun_1634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTIKMVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKN
          LTIKMVHAEAFSRPLSRNEVVGLIFRL.IFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKN
Retrocopy LTIKMVHAEAFSRPLSRNEVVGLIFRLMIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKN

Parental  VKLSEYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPG
          VKLSEYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPG
Retrocopy VKLSEYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPG

Parental  CGKTLIAKATAKEAGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDH
          CGKTLIAKATAKEAGC.FINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDH
Retrocopy CGKTLIAKATAKEAGC*FINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDH

Parental  EATAMMKAQFMSLWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAILKLILKNE
          EATAMMKAQFMSLWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAILKLILKNE
Retrocopy EATAMMKAQFMSLWDGLDTDHSCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAILKLILKNE

Parental  NVDRHVDLLEVAQETDGFSGSDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKS
          NVDRHVDLLEVAQETDGFSGSDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKS
Retrocopy NVDRHVDLLEVAQETDGFSGSDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKS

Parental  KDAAFQNVLTHVCLD
          KDAAFQNVLTHVCLD
Retrocopy KDAAFQNVLTHVCLD

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	0.66 RPM	14.24 RPM
SRP017611_kidney	0.51 RPM	9.73 RPM
SRP017611_liver	0.08 RPM	4.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1634 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1634 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1634 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005296	1 retrocopy	retro_cjac_1101,
Homo sapiens	ENSG00000138138	1 retrocopy	retro_hsap_1900,
Gorilla gorilla	ENSGGOG00000026651	1 retrocopy	retro_ggor_1393,
Macaca mulatta	ENSMMUG00000006414	1 retrocopy	retro_mmul_608,
Nomascus leucogenys	ENSNLEG00000012135	1 retrocopy	retro_nleu_1231,
Oryctolagus cuniculus	ENSOCUG00000012082	1 retrocopy	retro_ocun_1634 ,
Pan troglodytes	ENSPTRG00000002717	1 retrocopy	retro_ptro_1255,
Pteropus vampyrus	ENSPVAG00000014020	1 retrocopy	retro_pvam_1080,
Rattus norvegicus	ENSRNOG00000010861	1 retrocopy	retro_rnor_2752,
Ictidomys tridecemlineatus	ENSSTOG00000006563	1 retrocopy	retro_itri_309,