RetrogeneDB ID: retro_rnor_2752

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: AABR06111059.1:41..752(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Atad1
• Ensembl ID: ENSRNOG00000010861
• Aliases: Atad1, Ab2-088
• Description: ATPase family AAA domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q505J9]

Sequence

>retro_rnor_2752
ATGGTACATGCTGAAGCCTTTTCTCGTCCATTGAGTCGGAATGAAGTTGTCGGTTTAATTTTCCGTTTAACAATATTTGG
TGCAGTAACGTACTTCACTATTAAATGGATGGTAGATGCCATTGACCCCACCAGGAAGCAGAAGGTAGAAGCTCAGAAAC
AGGCGGAAAAACTGATGAAGCAAATTGGTGTGAAAAATGTGAAGCTTTCAGAATATGAAATGAGTATTGCTGCTCATCTA
GTAGACCCTCTTAATATGCATGTTACTTGGAGTGATATAGCAGGTTTAGATGACGTCATTACAGATCTGAAAGACACAGT
CATCTTACCTATCAAAAAGAAGCATTTGTTTGAGAATTCCAGACTACTGCAGCCTCCAAAAGGTGTTCTTCTGTATGGAC
CTCCAGGCTGTGGGAAAACATTAATTGCCAAAGCAACAGCCAAAGAAGCAGGCTGTCGGTTCATTAACCTCCAGCCTTCG
ACACTGACTGATAAGTGGTATGGAGAATCTCAAAAACTGGCTGCTGCTGTTTTCTCCCTTGCCATAAAGCTACAGCCTTC
TATCATATTTATTGATGAAATAGACTCTTTCCTACGAAATCGTTCCAGTTCTGACCACGAAGCTACAGCGATGATGAAAG
CTCAGTTTATGAGTCTCTGGGATGGACTGGACACTGATCACAGCTGCCAGGTTATAGTAATGGGAGCTACC

Alignment

ORF - retro_rnor_2752 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 65.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKNVKLS
          MVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKNVKLS
Retrocopy MVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKNVKLS

Parental  EYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKT
          EYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKT
Retrocopy EYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKT

Parental  LIAKATAKEAGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATA
          LIAKATAKEAGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATA
Retrocopy LIAKATAKEAGCRFINLQPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATA

Parental  MMKAQFMSLWDGLDTDHSCQVIVMGAT
          MMKAQFMSLWDGLDTDHSCQVIVMGAT
Retrocopy MMKAQFMSLWDGLDTDHSCQVIVMGAT

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	79.01 RPM
SRP017611_kidney	0.00 RPM	74.32 RPM
SRP017611_liver	0.00 RPM	31.67 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2752 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2752 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,