RetrogeneDB ID: retro_rnor_1787

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:45687193..45689313(+)
• Located in intron of: ENSRNOG00000005335

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_1787
ATGCCTGAGGAAGTGCACCATGGAGAGGAAGAGGTGGAGACCTTTGCCTTTCAGGCAGAAATTGCCCAGCTGATGTCCCT
CATCATCAACACTTTCTACCCAAACAAAGAGATTTTCCTTCAGGAGTTGATCTCTAATGTTTCTGATGCCCTGGACAAGA
TTCGATGTGAGAGCCTGACTGACCCTTCCAAGTTGGACAGCGGGAAAGAGCTGAAGATTGACATCATCCCCAAACCTCAG
GAGCGCACGCTGACTTTGGTGGACACAGGCATTGGCATGACCAAGGCTGACCTCATAAATAACTTGGGAACCATTGCTAA
GTCTGGTACAAAGGCGTTCATGGAGGCTCTCCAGGATGGTGCAGACATCTCCATAATTGGGCAGTTTGTTGTCGGCTTCT
ACTCTTCCTACCTGGTGGCAGAGAAAGTGGTTGTGATCACGAAGCACAACGATGATGAGCAGTATGCCTGGGAGTCTTCT
GCTGGTGGATCCTTCATCATCCGCGCAGACCACAGTGAGCCCATTGGCTGGGGTACCAAAGTGATCCTTCACCTCAAAGA
AGACCAGACAGAGTACTTAGAGGAGAGGAGGGTCAAGGAAGTGTTGAAGAAACACTCGCAGTTCATAGGCTATCCCATCA
CCCTCTACTTGGAGAAAGAACGAGAGAAGGAGATCAGTGATGATGAGGCAGAGGAAGAGAAAGGGGAGAAGGAGGAGGAA
GATAAGGAGGATTAGGAGAAGCCTAAGATTGAGGATGTGGGATCTGACGAGGAGGATGAGAGCAGCAAAGATAAGAAAAA
GAAAACAAAGAAGATCAAGGAGAAGTACATTGACCAGAAAGAGCTGAATAAGTCGAAGCCCAACTGGATCAGAAATCCTG
ATGACATCACCCAAGAGGAATATGGTGAATTCTATAAGAGCCTCATCAATGACTGGGAAGACCACTTGGCAGTCAAGCAC
TTCTCTGTAGAAGGGCAGTTGGAATTCAGGGCATTGCTCTTCATTCCCCAGCGAGCTCCCTTTGACCTCTTTGAGAACAA
CAAGAAGAAGAACAACATCAAATTGTATGTCCATCGTGTGTTCATCATGGACAGCTGTGATGAGCTGATACCTGAGTACC
TCAACTTCATCCATGGTGTGGTTGATTCTGAGGACCTGCCTCTGAACATCTCCTGAGAAATGCTCCAGCAGAGCAAGATC
CTGAAAGTCATCTGCAAGAACATTGTGAAGAAGTGCCTTGAGTTCTTCTCTGAGTTGGCTGAAGACAAAGAGAACTACAA
GAAATTTTATGAGGCATTCTCCAAGAATTTAAAACTTGGAATCCATGAGGATTCCACTAACCGTTGCCACCTCTCTGAGC
TCCTTCACTACCATAACTCTCAGTCTGGAGATGAGATGACTTCCCTGTCAGAGTATGTGTCTCGCATAAAGGAGACACAG
AAGTCCATCTACTATATCACTGGTGAGAGCAAAGAGCATGTGGCCAACTTTGCCTTCATGGAGCGTGTGTGGAAACAGGG
CTTTGAGGTGGTGTACATGACTGAGCCCATTGAGAGTACTGAGTGCAGCAGCTCAAGGAGTTCGATGGCAAGAGCCTGGT
CTCTGTGACCAAGGAGGTCCTGGAGCTACCAGAAGATGAGGAAGAGAAAAAGAAAATGGAGGAGAGCAAGGCAAAGTTTG
AGAATCTCTGCAAACTCATGAAGGAGATCTTGGACAAGAAGATTGAAAGAGTGACTATCTCCAATAGGCTTGTGTCTTCA
CCCTGCTGCATTGTGACAAGCACCTATGGCTGGACAGCCAACATGGAACAGATCGTGAAGGCCCGGGCACTGCGAGACAA
CTCTACAATGGAATACGTGATGGCCAAGAAACACCTAGACATCAACCCTGACCACCCCATGGTGGAGACTCTGCTGCAGA
AGGCTCAGGCAGACAAAAACGACAAAGCTGTCAAAGACCTGGTGGTGCTGCTGTTTGAGACTGCTCTGCTCTCCTCTGGC
TTCTCACTTGAGGACCCCCAAACCAACTCCAACTGCATCTACCGCATGATTAAACTAGGCCTGGGCATTGATGAAGATGA
GGTCACTGCAGAAGAGCCCAGTGCTGCTGTTCCTGATGAG

Alignment

ORF - retro_rnor_1787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.41 %
• Parental protein coverage: 97.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKE
          MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFY.NKEIFL.ELISN.SDALDKIR.ESLTDPSKLDSGKE
Retrocopy MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYPNKEIFLQELISNVSDALDKIRCESLTDPSKLDSGKE

Parental  LKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVA
          LKIDIIP.PQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQ.GADIS.IGQF.VGFYS.YLVA
Retrocopy LKIDIIPKPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQDGADISIIGQFVVGFYSSYLVA

Parental  EKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIG
          EKVVVITKHNDDEQYAWESSAGGSF..RADH.EPIG.GTKVILHLKEDQTEYLEERRVKEV.KKHSQFIG
Retrocopy EKVVVITKHNDDEQYAWESSAGGSFIIRADHSEPIGWGTKVILHLKEDQTEYLEERRVKEVLKKHSQFIG

Parental  YPITLYLEKEREKEISDDEAEEEKGEKEEEDKEDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQE
          YPITLYLEKEREKEISD....................PKIEDVGSDEED.S.KDKKKKTKKIKEKYIDQ.
Retrocopy YPITLYLEKEREKEISDXXXXXXXXXXXXXXXXXXXXPKIEDVGSDEEDESSKDKKKKTKKIKEKYIDQK

Parental  ELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKK
          ELNK.KP.W.RNPDDITQEEYGEFYKSL.NDWEDHLAVKHFSVEGQLEFRALLFIP.RAPFDLFEN.KKK
Retrocopy ELNKSKPNWIRNPDDITQEEYGEFYKSLINDWEDHLAVKHFSVEGQLEFRALLFIPQRAPFDLFENNKKK

Parental  NNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELA
          NNIKLYV.RVFIMDSCDELIPEYLNFI.GVVDSEDLPLNIS.EMLQQSKILKVI.KNIVKKCLE.FSELA
Retrocopy NNIKLYVHRVFIMDSCDELIPEYLNFIHGVVDSEDLPLNIS*EMLQQSKILKVICKNIVKKCLEFFSELA

Parental  EDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGES
          EDKENYKKFYEAFSKNLKLGIHEDSTNR..LSELL.YH.SQSGDEMTSLSEYVSR.KETQKSIYYITGES
Retrocopy EDKENYKKFYEAFSKNLKLGIHEDSTNRCHLSELLHYHNSQSGDEMTSLSEYVSRIKETQKSIYYITGES

Parental  KEQVANSAFVERVRKRGFEVVYMTEPID-EYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAK
          KE.VAN.AF.ERV.K.GFEVVYMTEPI..EY.VQQLKEFDGKSLVSVTKE.LELPEDEEEKKKMEESKAK
Retrocopy KEHVANFAFMERVWKQGFEVVYMTEPIE<EY*VQQLKEFDGKSLVSVTKEVLELPEDEEEKKKMEESKAK

Parental  FENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEIN
          FENLCKLMKEILDKK.E.VTISNRLVSSPCCIVTSTYGWTANME.I.KA.ALRDNSTM.Y.MAKKHL.IN
Retrocopy FENLCKLMKEILDKKIERVTISNRLVSSPCCIVTSTYGWTANMEQIVKARALRDNSTMEYVMAKKHLDIN

Parental  PDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVTAEE
          PDHP.VETL.QKA.ADKNDKAVKDLVVLLFETALLSSGFSLEDPQT.SN.IYRMIKLGLGIDEDEVTAEE
Retrocopy PDHPMVETLLQKAQADKNDKAVKDLVVLLFETALLSSGFSLEDPQTNSNCIYRMIKLGLGIDEDEVTAEE

Parental  PSAAVPDE
          PSAAVPDE
Retrocopy PSAAVPDE

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	0.50 RPM	1259.12 RPM
SRP017611_kidney	0.42 RPM	937.38 RPM
SRP017611_liver	0.07 RPM	517.80 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1787 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1787 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1787 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,