RetrogeneDB ID: retro_rnor_1562

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:200709279..200711427(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hsp90ab1
• Ensembl ID: ENSRNOG00000019834
• Aliases: Hsp90ab1, HSP90-BETA, HSP90B, HSPC2, Hspcb
• Description: Heat shock protein HSP 90-beta [Source:UniProtKB/Swiss-Prot;Acc:P34058]

Sequence

>retro_rnor_1562
CCTGAGGAAGTGCACCATGGAGAAGAAGAAGTGGAGACCTTTGCCTTTTAGGCAGAAATTGCCCAGCTGACGTCCCTCAT
CATCAACACTTTCTACTCAAACAAGGAGATTTTCCTCTGGGAGTTGATCTCTAATGCTTCTGATGCCCTGGACAAGATTC
AGTATGAAAGCCTGACGGATCTTTCCAAGTTGGAAAGTCAGAAAGAGCTAATGATTGACATCATTCCCAACCCTCAGGAG
CACATGCTGACATTGGTAGACACAGGCATTGGCATGGCCAAGACTGATCTCAGAAACAACTTGGGAACCATTGCTATGTC
TGGTACAAAGGCATTCATGGAGGTTCTCCAGGCTGGTGCAGACATCTCCATGATTGGGCAGTTTGGTGTCAGCTTCTACT
CTGCCTATCTGGTGGTAGATGAAGTGGTTGTGGTCACGAAGCACAACGATGACGAGCAGTATGCCTGGGAGTCTTCTGCT
GGTGGATCCTTCACCGTTCATGCAGACCGTGGTGAGCCCATTGGCTGGGGTACCCAAGTGATCCTTCACCTCAAAGAAGA
TCAGACAGAGTACTTAGAGGAGAGGAGGGTCAAGGAAGTGGTGAAGAAACACTTGAAGTTCATAGGCTACCTCATCACCT
CTACCTGGAGAATGAAGGAGAGAAGAACAGTGATGATGAGGCAGAGGAAGAGAAAGGGGAGAAAGGGGAGGAAGATAAGG
AGGATGAGGAGCCTAAGATTGAGAATGTGGGATCTGACGAGGAGGATGAGAGTGTCAAAGATAAGAAAAAGAAAACAAAG
AAGATCAAGGAGAATTACATTGACCAGGAAGAGGTGAATAAGACGAATCTTATCTGGACCAGAAATCCGGATGACATCAT
TCAAGAGGAAAATGGTGAATTCTATAAGATCCTCACCAATGACTGGGAAGACCACTTGACAGTCAAGCACTTCTCTGTAG
AAATGCAGTTGGAATTCAAGGCATTGCTCTTCATTCCCTGGCGAGCTCCCTTTGACCTCATTGAGAACAAGAAGAAGAAT
AACAACATCAAATTGTATGTCCGTCGTGTGTTCATCATGGACAGCTGTGATGAGCTGATACCTGAGTACCTCAACTGCAT
CCGTGGTGTGGCTGATTCTGAGGACCTGCCCCTGAATATCTCCCAAGAAATGCTCCAGCAGAGTAAGATCCTGAAAGTCA
TCCACAAGAACATTGTGAAGAAGTACCTTGAGCTCTTCTCTGAGTTGGCTGAAGACAAAGAGAACTACAAGAAATTCTCC
AAGAATTTAAGGCTTAGAATCCATGAGGATTCCACTAACCATAGCCGCCTCTCTGAGCTCCTTCACTACCACACCTCTCA
GTCTGGAGATGAGATGACTCCCTGTCAGAGTATGTGTCTCACATGAAGGAGACACAGAAGTCCATCTACCACATCACTGG
TGAGAGGAAAGAGGAAGAGGCCAACTCTGCCTTTGTGGAGTGTGTGCGGAAACGAGGCTTTGAGGTGGTGAATATGACTG
AGCCCATTGATGAGCACTGCGTGCAGCAGCTCAAGGAATCCAACGACAAAAGCCTGGTCTCAGTGATGAAGGAGGGCCTG
GAACTACCAGAGGATGAGGAAGAGATGAAGAAAATGGAGGAGAGCAAGGCAAAGTTTGAGAATCTCTGCAAGCTCATGAA
GGAGATCTTGGACAAGAAGATTGAAAGAGTGACTATCTCCAATAGGCTTGTGTCTTCACCCTGCTGCAGTGTGACAAGCA
CCTATGGCTGGACAGCCAACACGGAACAGATCGTGAAGGCTCAGGCACTGCGAGACAATTCTACAATGGAATACGTGATG
GCCAAGAAACACCTAGAGATCAACCCTGACCACCCCATGGTGGAGACTCTGCTGCAGAAGGCTGAGGCAGACACAAATGA
CAAAGCTGTCAAAGACCTGGTGGTGCTTCTGTTTGAAACGGCTCTGCTCTCCTCTGGCTTCTCACTTGAGGACCCCCAAA
CCCACTCCAACGGCATCTACCGCATGATTAAACTAGGCCTGGGCATTGATGAAGATGAGGTTCCTGCAGAAGAGCCCAGT
GCTGCTGTTCCTGATGAGATCCCCCCATGGAGGGTGATGAGGATGCCTCTGGCATGGAAGAAGTGGAT

Alignment

ORF - retro_rnor_1562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.95 %
• Parental protein coverage: 99.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKEL
          PEEVHHGEEEVETFAF.AEIAQL.SLIINTFYSNKEIFL.ELISNASDALDKI.YESLTD.SKL.S.KEL
Retrocopy PEEVHHGEEEVETFAF*AEIAQLTSLIINTFYSNKEIFLWELISNASDALDKIQYESLTDLSKLESQKEL

Parental  KIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAE
          .IDIIPNPQE..LTLVDTGIGM.K.DL.NNLGTIA.SGTKAFME.LQAGADISMIGQFGV.FYSAYLV..
Retrocopy MIDIIPNPQEHMLTLVDTGIGMAKTDLRNNLGTIAMSGTKAFMEVLQAGADISMIGQFGVSFYSAYLVVD

Parental  KVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGY
          .VVV.TKHNDDEQYAWESSAGGSFTV.AD.GEPIG.GT.VILHLKEDQTEYLEERRVKEVVKKH..FIGY
Retrocopy EVVVVTKHNDDEQYAWESSAGGSFTVHADRGEPIGWGTQVILHLKEDQTEYLEERRVKEVVKKHLKFIGY

Parental  PIT-LYLEKEREKEISDDEAEEEKGEKEEEDKEDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQE
          .IT.LYLE.E.EK..SDDEAEE.........KEDEE.PKIE.VGSDEED.S.KDKKKKTKKIKE.YIDQE
Retrocopy LIT<LYLENEGEKN-SDDEAEEXXXXXXXXXKEDEE-PKIENVGSDEEDESVKDKKKKTKKIKENYIDQE

Parental  ELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKK
          E.NKT..IWTRNPDDI.QEE.GEFYK.LTNDWEDHL.VKHFSVE.QLEF.ALLFIP.RAPFDL.ENKKK.
Retrocopy EVNKTNLIWTRNPDDIIQEENGEFYKILTNDWEDHLTVKHFSVEMQLEFKALLFIPWRAPFDLIENKKKN

Parental  NNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELA
          NNIKLYVRRVFIMDSCDELIPEYLN.IRGV.DSEDLPLNIS.EMLQQSKILKVI.KNIVKK.LELFSELA
Retrocopy NNIKLYVRRVFIMDSCDELIPEYLNCIRGVADSEDLPLNISQEMLQQSKILKVIHKNIVKKYLELFSELA

Parental  EDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMT-SLSEYVSRMKETQKSIYYITGE
          EDKENYKK....FSKNL.L.IHEDSTN..RLSELL.YHTSQSGDEMT.SLSEYVS.MKETQKSIY.ITGE
Retrocopy EDKENYKK----FSKNLRLRIHEDSTNHSRLSELLHYHTSQSGDEMT<SLSEYVSHMKETQKSIYHITGE

Parental  SKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAK
          .KE..ANSAFVE.VRKRGFEVV.MTEPIDE.CVQQLKE...KSLVSV.KEGLELPEDEEE.KKMEESKAK
Retrocopy RKEEEANSAFVECVRKRGFEVVNMTEPIDEHCVQQLKESNDKSLVSVMKEGLELPEDEEEMKKMEESKAK

Parental  FENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEIN
          FENLCKLMKEILDKK.E.VTISNRLVSSPCC.VTSTYGWTAN.E.I.KAQALRDNSTM.Y.MAKKHLEIN
Retrocopy FENLCKLMKEILDKKIERVTISNRLVSSPCCSVTSTYGWTANTEQIVKAQALRDNSTMEYVMAKKHLEIN

Parental  PDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVTAEE
          PDHP.VETL.QKAEAD.NDKAVKDLVVLLFETALLSSGFSLEDPQTHSN.IYRMIKLGLGIDEDEV.AEE
Retrocopy PDHPMVETLLQKAEADTNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNGIYRMIKLGLGIDEDEVPAEE

Parental  PSAAVPDEI-PPLEGDEDASRMEEVD
          PSAAVPDEI.PP.EGDEDAS.MEEVD
Retrocopy PSAAVPDEI<PPMEGDEDASGMEEVD

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	1259.12 RPM
SRP017611_kidney	0.00 RPM	937.38 RPM
SRP017611_liver	0.00 RPM	517.80 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1562 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
Homo sapiens	ENSG00000096384	2 retrocopies	retro_hsap_2912, retro_hsap_2958,
Macropus eugenii	ENSMEUG00000013735	1 retrocopy	retro_meug_1896,
Myotis lucifugus	ENSMLUG00000005239	2 retrocopies	retro_mluc_1604, retro_mluc_865,
Macaca mulatta	ENSMMUG00000022686	2 retrocopies	retro_mmul_1319, retro_mmul_1869,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
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,
Tursiops truncatus	ENSTTRG00000006924	1 retrocopy	retro_ttru_292,