RetrogeneDB ID: retro_rnor_454

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:81226006..81226263(+)
• Located in intron of: ENSRNOG00000014788

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hn1
• Ensembl ID: ENSRNOG00000003661
• Aliases: None
• Description: Hematological and neurological expressed 1 protein [Source:UniProtKB/Swiss-Prot;Acc:Q6AXU6]

Sequence

>retro_rnor_454
GCCAAGTCTAGTGGTGGCAGGGAAGATTCGGAGTCGCCTGGAACACAGAGAAGTAACTTCTGAAACAAGCTCTGGAGATT
TCTTAGACCTCAAGGGAGAAGGTGATACGCATGAAAATGTGGACACAGACTTCCAAGGCAACCTGGCATAGATGGAAGAG
AGCAGGTGCCTGCTGCTCCTGTGCCCAGACCAGTGGCTTGGGCCCCAGCACCATCCAGGAGAAAACCCCTGGCGGCAAGT
CCAACCTGGTCTTGGGT

Alignment

ORF - retro_rnor_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 58.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AKSAGGREDSESPGTQRSN-SSEASSGDFLDLKGESDVHENVDTDFQASLAQVEE-KPVPAAPVPSPVAP
          AKS.GGREDSESPGTQRSN.S...S.GDFLDLKGE.D.HENVDTDFQ..LA..EE...VPAAPVP.PVA.
Retrocopy AKSSGGREDSESPGTQRSN>SETSS-GDFLDLKGEGDTHENVDTDFQGNLA*MEE<EQVPAAPVPRPVAW

Parental  APAPSRRNP-PGGKSSLVLG
          APAPSRR.P.PGGKS.LVLG
Retrocopy APAPSRRKP<PGGKSNLVLG

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	0.07 RPM	45.58 RPM
SRP017611_kidney	0.00 RPM	20.66 RPM
SRP017611_liver	0.00 RPM	6.25 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_454 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_454 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014553	1 retrocopy	retro_cjac_2715,
Echinops telfairi	ENSETEG00000013294	1 retrocopy	retro_etel_89,
Homo sapiens	ENSG00000189159	1 retrocopy	retro_hsap_2343,
Gorilla gorilla	ENSGGOG00000013996	1 retrocopy	retro_ggor_1780,
Mustela putorius furo	ENSMPUG00000013971	1 retrocopy	retro_mputfur_1200,
Mus musculus	ENSMUSG00000020737	6 retrocopies	retro_mmus_1096, retro_mmus_2442, retro_mmus_2574, retro_mmus_3706, retro_mmus_864, retro_mmus_934,
Nomascus leucogenys	ENSNLEG00000000610	1 retrocopy	retro_nleu_348,
Oryctolagus cuniculus	ENSOCUG00000002950	2 retrocopies	retro_ocun_1647, retro_ocun_457,
Ochotona princeps	ENSOPRG00000010887	2 retrocopies	retro_opri_537, retro_opri_88,
Pan troglodytes	ENSPTRG00000024246	1 retrocopy	retro_ptro_1715,
Rattus norvegicus	ENSRNOG00000003661	2 retrocopies	retro_rnor_1794, retro_rnor_454 ,
Ictidomys tridecemlineatus	ENSSTOG00000015171	1 retrocopy	retro_itri_1449,