RetrogeneDB ID: retro_rnor_1561

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:196981397..196982679(+)
• 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_1561
ATGCCTGAGGAAGTTCACCATGGAAAGGAAGAGGTGGAGACCTTTGCCTTTCAGGCAGAAATTGCCTAGCTGATGTCCCT
CATCATCAACACTTTCTACTCAAACAAGGAGATTTTCTGGGAGTTGATCTCCAATGCTTCTGATGCCCTGGACAAGATTC
AGTATGAGAGCCTGACCACCCTTTCAAGTTGTTCAGCGGGAAAGAGCTAAAGATTGGCATCGTCCCAAACCCTCAGGAGC
GCATGCTGACTTTGGTGGACATAGGCATTGGCATGACCAAGGCTGACCTCATAAATAACTTGGGAACCATTGCTAGGTCT
GGTACAAAGGCGTTCATGGAGGCTCTCCAGGCTGGTGCAGACATCTCCATGATTGGGCAGTTTGGTGTTGGCTTCTACTC
TGCCTACCTGGTGGCGGAGAAAGTGGTTGTGGTCACAAAGCACAACGATGACGAGCAGTATGCCTGGGAGTCTTCTGCTG
GTGGATCCTTCACTGTCCATGCAGACCATGGTGAGCCTTTGGCTGGGGTACCAAAGTGATCCTTCACCTCAAAGAAGACC
AGACAGAGTACTTAGAGGAGAGGAGGGTCAAGGAAGTGGTGAAGAAACACTTGCAGTTCATAGACTACCTCTTCACCCTC
TACCTGGAGAAGGAATGAGAGAAGGAGAACAGTGATGATGAGGCAGAGGAAGAAAAAGGGGAGAAAGGGAAGGAAGATAA
GGAGGATGAGGAAAAGCCTAAGACTGAGGATGTAGGATCTAATGAGGAAGATGAGAATGGCAAAGATAAGAAAAAGAAAA
CAAAGAAGATCAAGGAGAAGTACATTGACCAGGAAGAGCTGAATAAGACGAAGCCTATCTGGACCAGAAATCCTAATGAC
ATCACTCAAGAGGAATATGGTGAATTCTATAAGATCCTCACCAATGACTGGAAAGATCACTTGATAGTCAAGCACTTCTT
TGTAGAAGGGCAGTTGGAATTCAGGGCATTGCTCTTCATTCCCTGGCGAGCTCCCTTTGACTTCTTTAAGAACAAGAAAG
AAAAGAACAACATCAAATTTTATGTCCGTTGTGTATTCATCATGGACAGCTGTGATGAGCTGATACCTGAGTACATCAAC
TGCATCCGTGGTGTGGCTGACTCTGAGGACCTGCCCCTGAACATCTCCTGAGAAATGGTCCAGCAGAGCAAGATCCTGAA
AATCATCTGCAAGAGCATTGTGAAGAACTGCCTAGAGCTCTTCTCTGAGTTGGCTGAAGACAAAGAGAAGTATAAGAAAT
TC

Alignment

ORF - retro_rnor_1561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.94 %
• Parental protein coverage: 59.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTD-PSKLDSGK
          MPEEVHHG.EEVETFAFQAEIA.LMSLIINTFYSNKEIF..ELISNASDALDKI.YESLT..P.KL.SGK
Retrocopy MPEEVHHGKEEVETFAFQAEIA*LMSLIINTFYSNKEIFW-ELISNASDALDKIQYESLTT<PFKLFSGK

Parental  ELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLV
          ELKI.I.PNPQER.LTLVD.GIGMTKADLINNLGTIA.SGTKAFMEALQAGADISMIGQFGVGFYSAYLV
Retrocopy ELKIGIVPNPQERMLTLVDIGIGMTKADLINNLGTIARSGTKAFMEALQAGADISMIGQFGVGFYSAYLV

Parental  AEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPI-GRGTKVILHLKEDQTEYLEERRVKEVVKKHSQF
          AEKVVV.TKHNDDEQYAWESSAGGSFTV.ADHGEP..G.GTKVILHLKEDQTEYLEERRVKEVVKKH.QF
Retrocopy AEKVVVVTKHNDDEQYAWESSAGGSFTVHADHGEPL<GWGTKVILHLKEDQTEYLEERRVKEVVKKHLQF

Parental  IGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKEDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYID
          I.Y..TLYLEKE.EKE.SDDEAEEEKGEK..EDKEDEEKPK.EDVGS.EED..GKDKKKKTKKIKEKYID
Retrocopy IDYLFTLYLEKE*EKENSDDEAEEEKGEKGKEDKEDEEKPKTEDVGSNEEDENGKDKKKKTKKIKEKYID

Parental  QEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKK
          QEELNKTKPIWTRNP.DITQEEYGEFYK.LTNDW.DHL.VKHF.VEGQLEFRALLFIP.RAPFD.F.NKK
Retrocopy QEELNKTKPIWTRNPNDITQEEYGEFYKILTNDWKDHLIVKHFFVEGQLEFRALLFIPWRAPFDFFKNKK

Parental  KKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSE
          .KNNIK.YVR.VFIMDSCDELIPEY.N.IRGV.DSEDLPLNIS.EM.QQSKILK.I.K.IVK.CLELFSE
Retrocopy EKNNIKFYVRCVFIMDSCDELIPEYINCIRGVADSEDLPLNIS*EMVQQSKILKIICKSIVKNCLELFSE

Parental  LAEDKENYKKF
          LAEDKE.YKKF
Retrocopy LAEDKEKYKKF

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	1259.12 RPM
SRP017611_kidney	0.00 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_1561 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1561 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,