RetrogeneDB ID: retro_rnor_860

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:12857102..12858446(+)
• Located in intron of: ENSRNOG00000049143

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hsp90aa1
• Ensembl ID: ENSRNOG00000007219
• Aliases: Hsp90aa1, Hsp86, Hsp90, Hspca
• Description: Heat shock protein HSP 90-alpha [Source:UniProtKB/Swiss-Prot;Acc:P82995]

Sequence

>retro_rnor_860
TACATTGATCAAGAAGAACTCAACAAAACAAAGCCAAATTGTACAAGAAATCCTGATGACATTACATAAGAATATGGACA
GTTCTTCAAAAGCTTAGCCAACGATTGGGAAGAACATTGGGCAGTAAAGAATTTTTCTGTTGAAGGATAATTAGAATCCC
GGGTCATTCTTTTTGTACCAAGATGGGCTCCTTTTGATCTGTTTGAAAACAGAAAGAAAAAGAAGAACATCAAGTTGTAT
GTTTGTAGTATTTTTATCATGGATAACTATGAGGAGTTAATCTCTGAGTATCTGAATTTCATCAGAGGGGTGGTGGATTT
TGTGGATCTCCCTCTAAATATTTCCCATGAAATGCTGCAACAAAGCAAAATTCTGGAAGTTATCAGAAAGAATTTCGTCA
AGAAATTCTTAGAACTATTTACTGAACTGGCTGAAGATAAAGAGAACTACAAAAAGTGTTATGAGCAATCCTCAAAAATT
ATAAAGTTTGGAATTCATGAAGACTCTCAAAATTGGAAGAAGCCTTCAGAGCTGTTGAGATACTACACATCTGCTTCTGG
GGATGAGATGGTTTCTCTGAAGGACTACTGCACCAGAATGAAGGAAAACCAGAAGCACATCTATTTTTATCACAGGTGAG
ACCAAGGACCAGGTTGATAACTCAGCCTTTGTGGAACCTCTTCAAAAGCATAGCTTAGAAGTAATCTATATGATTGAGCC
CATTGATGAGTATTGTGTGCAACAGCTGAAGGAATTTGAGGACAAGACCTTGATGTCAGTTACAAAACAAGGACAGGAAC
TTCCAGGGAATGAAGAGAAAAAGAAGAAAAAAGGAGAAAAAAAGACAAAATTTAAGAACCTGTGAAAAATTATGAAAGAT
ATTTTGGAGAAAAGGGTTGAAAAAGTGGTTGTGTCAAACCAATTGGTGACATCCCTATGCTGTATTGTCACAAGCACATA
TGGGCAAACAGAAAATATGGAAGAATCATGAAAGTTCAAGCATCAAGCACTCAAAGACAACTCAACAATGAGTTACATGG
CAGCAAAGACACACTTGGAGATAAACCCTGACCACTCCATTATTGAAACAAAGCAAAAGGCAGAGGCTGAAAAGAATGAC
AAGTCATGAAGGATCTGGTCATCTTGATGTATGAAAATGCACTCCTGTCTTCTAGCATCTGCCTGGAAGATCCCCAAACC
CATGCTAACAGGATCTACACTATGATCAAGTTTTGTTTAGGTACTGATGAGGATGATCCTACAGTGGATGATACCAATGC
TGTTGTAACTGAAGAAATGCCACCCCTGGAGGGAGATGATGACACATCATGCATGGAAGAAGTA

Alignment

ORF - retro_rnor_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.31 %
• Parental protein coverage: 61.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEEHLAVKHFSVEGQLEFRALLFVPRRAPFDLFE
          YIDQEELNKTKP..TRNPDDIT.E.YG.F.KSL.NDWEEH.AVK.FSVEG.LE.R..LFVPR.APFDLFE
Retrocopy YIDQEELNKTKPNCTRNPDDIT*E-YGQFFKSLANDWEEHWAVKNFSVEG*LESRVILFVPRWAPFDLFE

Parental  NRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLEL
          NRKKK.NIKLYV...FIMDN.EELI.EYLNFIRGVVD..DLPLNIS.EMLQQSKIL.VIRKN.VKK.LEL
Retrocopy NRKKKKNIKLYVCSIFIMDNYEELISEYLNFIRGVVDFVDLPLNISHEMLQQSKILEVIRKNFVKKFLEL

Parental  FTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYF
          FTELAEDKENYKK.YEQ.SK.IK.GIHEDSQN.KK.SELLRYYTSASGDEMVSLKDYCTRMKENQKHIYF
Retrocopy FTELAEDKENYKKCYEQSSKIIKFGIHEDSQNWKKPSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYF

Parental  -ITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEEKKKQE
          .ITGETKDQV.NSAFVE.L.KH.LEVIYMIEPIDEYCVQQLKEFE.KTL.SVTK.G.ELP..........
Retrocopy >ITGETKDQVDNSAFVEPLQKHSLEVIYMIEPIDEYCVQQLKEFEDKTLMSVTKQGQELPGNXXXXXXXX

Parental  EKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERI--MKAQALRDNSTMGYMAA
          .....F.NL.KIMKDILEK.VEKVVVSN.LVTS.CCIVTSTYG.T.NME.....K.QAL.DNSTM.YMAA
Retrocopy XXXXXFKNL*KIMKDILEKRVEKVVVSNQLVTSLCCIVTSTYGQTENMEES*KFKHQALKDNSTMSYMAA

Parental  KKHLEINPDHSIIETLRQKAEADKNDKS-VKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGID
          K.HLEINPDHSIIET..QKAEA.KNDKS..KDLVIL.YE.ALLSS...LEDPQTHANRIY.MIK..LG.D
Retrocopy KTHLEINPDHSIIET-KQKAEAEKNDKS<MKDLVILMYENALLSSSICLEDPQTHANRIYTMIKFCLGTD

Parental  EDDPTVDDTSAAVTEEMPPLEGDDDTSRMEEV
          EDDPTVDDT.A.VTEEMPPLEGDDDTS.MEEV
Retrocopy EDDPTVDDTNAVVTEEMPPLEGDDDTSCMEEV

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	533.11 RPM
SRP017611_kidney	0.00 RPM	216.81 RPM
SRP017611_liver	0.81 RPM	71.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_860 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_860 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006270	1 retrocopy	retro_btau_501,
Canis familiaris	ENSCAFG00000018036	1 retrocopy	retro_cfam_1094,
Callithrix jacchus	ENSCJAG00000033945	8 retrocopies	retro_cjac_1818, retro_cjac_2300, retro_cjac_2835, retro_cjac_3514, retro_cjac_3596, retro_cjac_3601, retro_cjac_3626, retro_cjac_502,
Cavia porcellus	ENSCPOG00000002015	1 retrocopy	retro_cpor_1372,
Homo sapiens	ENSG00000080824	2 retrocopies	retro_hsap_237, retro_hsap_859,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Monodelphis domestica	ENSMODG00000013302	3 retrocopies	retro_mdom_1653, retro_mdom_2010, retro_mdom_817,
Mus musculus	ENSMUSG00000021270	1 retrocopy	retro_mmus_2139,
Nomascus leucogenys	ENSNLEG00000015925	3 retrocopies	retro_nleu_714, retro_nleu_822, retro_nleu_854,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pan troglodytes	ENSPTRG00000006736	2 retrocopies	retro_ptro_207, retro_ptro_596,
Rattus norvegicus	ENSRNOG00000007219	1 retrocopy	retro_rnor_860 ,
Rattus norvegicus	ENSRNOG00000019834	6 retrocopies	retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,