RetrogeneDB ID: retro_rnor_89

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:6561519..6566289(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000042340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Thoc2
• Ensembl ID: ENSRNOG00000007315
• Aliases: Thoc2, RGD1561623
• Description: THO complex subunit 2 [Source:RefSeq peptide;Acc:NP_001178685]

Sequence

>retro_rnor_89
GTGGCGATGGCCTCGACAACTGTAGTGGTTCCTGCAGAGTGGATCAAGACCTGGGAGAAATCTGGGAGAGGCGAGTTTTT
GCGTTTATGCCGGATTCTCAGTGAAAGTAAAAGCCGTGACACTTTGGCTTGTAGAGATTTCCAGCAAGCACTCTATGAGT
TATCATACCATGTCATTAAAGGAACTTTAAAGCCCGAACAGGCCTCAAGTGTTCTTAATGACATCAGTGAATTTCGAGAA
GATATTCCGTTTATTCTTGCTGATATATTCTGCATATTAGATATTGAGACAAATTGCCTAGAAGAAAAAAGCAAGAGAGA
TCATTTTACACAACTGATATTAGCATGTTTATATTTAGTTTCAGACACAGTTCTGAAGGAACGCTTGGATCCAGAAACAT
TGGAATCATTAGGCCTTATCAAACAGTCTCAGCAATTCAATCAAAAATCAGTTAAGATCAAAACGAAACTCTTCTACAAA
CAGCAGAAGTTCAATTTGTTAAGAGAAGAAAATGAAGGTTATGCCAAGCTGATAGTTGAATTAGGGCAAGATTTATCTGG
GAGTATCACTAGTGATTTAATCTTAGAAATTCTCAAATCTTTAATAGGATGCTTTAATCTAGATCCCAACAGAGTTTTGG
ATATCATTTTAGAAGTGTTTGAATGCAGGCCAGAACACCATGATTTTTTTATATCTTTATTACAAGCTTATATGAGTATG
TGTGAACCACAGACACTGTGCCACATTCTTGGGTTCAAATTCAAGTTTTACCAGGAGCCAAATGGTGAGACTCCATCCTC
CTTGTATAGAGCTGCAGCAGTGCTCCTGCAGTTTAACCTTCTCGATTTGGATGATCTCTATGTGCACCTTCTTCCAGCTG
ATAGCTGCATCATGAATGAATACAAACGAGAAATTGTGGAAGCTAAGCAAATTGTTAAAAAACTTACAATGGTTGTGTTG
CCTTCCGAAAAAAGTGATGAGCGAGAGAAAGAAAAGAAAAAAGATGATAAAGTAGAGAAGGCACCTGACAATCAAAAACT
TGGTTTGTTGGAAGCCTTGTTAATTATTGGTGATTGGCAGCATGCTCAGAGTATTATGGACCGGATGCCTCCATACTATG
CCACATCACATAAAGTAATAGCCCTTGCTATTTGCAATCTTATACATATAACTATTGAACCTATTTACCGACGAGTTGGT
GTTCCTAAAGGTGCTAAAGGCTCACCTGTCAGCGCTTTACAAAACAAGAAGGCACCAAAGCAAGCAGAGAGCTTTGAAGA
CTTAAGAAGAGATGTTTTCAGCATGTTCTGTTACCTCGGTCCTCACCTTTCTCATGATCCCATCTTATTTGCAAAGGTTG
TGCGCATAGGCAAGTCATTTATGAAGGAGTTTCAGTCTGATGGGAAACAAGAAAATAAAGAGAAAATGGAAACTATCCTT
AGTTGTTTGCTTAGCGTTACCGACCAGGTGCTACTCCCATCCCTTTCTTTAATGGACTGCAATGCGTGCATGTCCGAGGA
ACTATGGGCAATGTTTAAGACATTCCCTTATCAGCATAGATACCGCTTATATGGACAGTGGAAGAATGAGACTTACAACA
GCCATCCACTTTTAGTGAAAGTTAAAGCTCATACTATAGACAGAGCCAAATACATCATGAAGCGTCTAACCAAGGAAAAT
GTGAAGCCTTCAGGAAGACAGATTGGAAAATTGAGCCACAGTAATCCAACCATTTTGTTTGATTATATCTTGTCACAAAT
ACAGAAGTATGATAACTTAATAACCCCTGTGGTAGACTCATTAAAATACCTCACTGCATTGAATTATGATGTTTTGGCCT
ACTGTATCATTGAAGCACTAGCTAATCCAGAAAAAGAAAGGATGAAACATGATGACACAACCATCTCCAATTGGCTGCAG
AGTTTGGCTAGTTTCTGTGGTGCAGTTTTTCGTAAATACCCAATTGACCTTGCTGGTCTTCTTCAGTATGTAGCCAATCA
GTTAAAGGCAGGCAAAAGTTTTGACCTGCTTATATTGAAAGAAGTGGTACAAAAAATGGCAGGTATAGAAGTTACAGAAG
AAATGACAATGGAGCAGCTTGAGGCTATGACAGGCGGGGAGCAACTGAAAGCTGAAGGTGGATATTTTGGCCAGATTAGA
AACACTAAAAAATCCTCTCAGAGGTTAAAGGATGCACTACTGGACCATGATCTTGCCCTTCCTCTTTGTTTGCTCATGGC
ACAGCAGAGGAATGGGGTGATCTTTCAGGAAGGCGGAGAGAAACATTTGAAACTTGTAGGAAAGCTATATGACCAGTGTC
ATGATACCTTGGTACAGTTCGGTGGATTTTTAGCATCAAATCTAAGCACAGATGATTACATAAAGAGAGTACCTTCAATC
GATGTTCTTTGTAATGAATTTCATACACCCCATGATGCAGCATTTTTTCTGTCTCGGCCAATGTATGCACACCATATTTC
ATCCAAGTATGATGAACTTAAGAAATCAGAAAAGGGTAGTAAGCAGCAACACAAAGTTCATAAGTACATTACATCATGTG
AGATGGTGATGGCTCCTGTTCATGAAGCAGTAGTCTCATTACACATCTCCAAAGTCTGGGAAGATATCAGCCCTCAGTTC
TACACCACATTCTGGTCTCTGACCATGTATGACCTTGCAGTTCCACATACCAGCTATGAACGGGAAGTCAATAAACTGAA
GATACAGATGAAAGCAGTTGATGACAATCAGGAAATGCCTCTAAATAAAAAGAAAAAGGAGAAAGAGCGCTGCACTGCCC
TGCAGGACAAGCTTCTTGAGGAAGAAAAGAAACAGATGGAGCATGTACAGCGAGTTCTACACAGACTGAAATTGGAAAAG
GACAACTGGCTCTTAGCAAAATCTACTAAAAATGAGACCATCACAAAATTTCTCCAGTTGTGTATATTTCCTCGATGTAT
TTTTTCAGCAATTGATTCTGTTTACTGTGCTCATTTTGTCGAGTTAGTCCATCAACAGAAGACTCCAAACTTCTCCACAC
TTCTTTGCTATGACCGAGTTTTCTCAGACATAATTTACATGGTTGCTAGCTTTACTGAAAATGAAGCTAGTCGATATGGG
AGATTTCTTTGCTGCATGTTAGAGACTGTGACTAGGTGGCACAGCGACAGATCCACCTATGAGAAAGAATGTGGAAACTA
TCCAGGATTCCTTACTATATTACGAGCAACCGGATTTGATGGTGGAAATAAAGCTGATCAGTTAGATTATGAGAATTTTC
GACATGTTGTACATAAATGGCATTACAAACTAACGAAGGCGTCGGTACATTGTCTTGAAACAGGCGAATATACTCATATC
AGGAATATTTTAATTGTACTAACAAAAATACTACCATGGTACCCCAAGGTTTTAAATCTGGGTCAGGCTTTGGAAAGAAG
AGTGCATAAAATCTGCCAAGAAGAGAAAGAAAAGAAACCAGATCTATATGCACTAGCAATGGTCTACTCTGGGCAGCTGA
AAAGTAGAAAGTCATACATGATACCTGAAAATGAATTTCATCACAAAGACCCTCCTCCAAGAAATGCTGCTACCAGTGTA
CAACCAAATGGGCCTTGTAGTGGGCTGCCTTCATCCATAGGAAGTACATCTAAATTAGATGAGAGCAGTGCTGAGGAGGC
CGACAAGTCACGAGAAAGATCTCAGTGTGCTGTGAAAGCTGTGAATAAAGCTTCCAGTGTCATACCAAAAGGGAACTTAA
GCAATGGAAATAGTGGCTCTAACACCAAAGCTGTTAAGGAAAATGACAAAGAAAAGGGCAAAGAGAAAGAAAAAGAGAAA
AAAGAAAAGGCCCCAGCTGTTACTCCAGAGGCTAGGGTACTTGGTAAAGACAGTAAAGAAAAACCCAAGGAAGAACAACC
AAATAAAGATGAAAAAATAAGAGAGGCCAAAGAAAGAATGCCTAAGTCTGATAAAGACAAGGAAAAATTAAAGAAGGAAG
AAAAGGCTAAAGATGAGAAATTTAGGATCATCGTCCCCAATGTAGAATCGAAATCCACTCAAGAAAGGGAAAAAGAGAAA
GAGCCCTCAAGAGAAAGAGATTTAGCAAAGGAAATGAAGTCAAAAGAGAATGTTAAAGGAGGAGAGAAAGCACCACTTTC
TGGTTCCTTGAAATCACCTGTTTCCCGAACAGATATCATAGAACCAGAAAGAGAAAAACGTCGCAAGGTTGATTCCCATC
CTTCTCCATCACATGCTTCCACAATAAAGGACAGTCTTGTTAAACTCAAGGAGTCTTCAGCAAAGCTCTATATCAACCAT
ATTCCACCACCATTGTGCAAGAGTAAGGAGAGAGAAGCAGACAAGAAAGATTTGGACAAATCAAGGGAAAGGTCCAGAGA
AAGGGAGAAAAAAGAGGAAAAGGACCGGAAAGAACGGAAAAGAGATTATTCAAACAATGACCGAGAGGCACCCCTGGACT
TAATCAAGAGGCGGAAAGATGAAAATGGAATATTGGGGGTTTCAAAACACAAAAGCGAAAGTCCCTGTGAGTCTCTTTAT
CCAAATGAGAAAGACAAGGAAAAAATTAAGTCAAAATCCTCAGGCAAAGAAAAAAGTGATTCATTTAAACCTGAAAAGAT
AGACAAAATATCCAGTGGGAAGAAGGAGTCCGGACATGACAAGGAAAAGATAGAGAAGAAAGAGAAATGGGACAGCTCTG
GAGATAAGGAAGAGAAGAAACATCATAAGTCTTCAGACAAGCATAGATAA

Alignment

ORF - retro_rnor_89 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAATVVVPAEWIKNWEKSGRGDFLHLCRILSENKSHDSSTYRDFQQALYELSYHVIKGNLKHEQASSVL
          MA..TVVVPAEWIK.WEKSGRG.FL.LCRILSE.KS.D....RDFQQALYELSYHVIKG.LK.EQASSVL
Retrocopy MASTTVVVPAEWIKTWEKSGRGEFLRLCRILSESKSRDTLACRDFQQALYELSYHVIKGTLKPEQASSVL

Parental  NDISEFREDMPSILADVFCILDIETNCLEEKSKRDYFTQLVLACLYLVSDTVLKERLDPETLESLGLIKQ
          NDISEFRED.P.ILAD.FCILDIETNCLEEKSKRD.FTQL.LACLYLVSDTVLKERLDPETLESLGLIKQ
Retrocopy NDISEFREDIPFILADIFCILDIETNCLEEKSKRDHFTQLILACLYLVSDTVLKERLDPETLESLGLIKQ

Parental  SQQFNQKSVKIKTKLFYKQQKFNLLREENEGYAKLIAELGQDLSGTITSDLILENIKSLIGCFNLDPNRV
          SQQFNQKSVKIKTKLFYKQQKFNLLREENEGYAKLI.ELGQDLSG.ITSDLILE..KSLIGCFNLDPNRV
Retrocopy SQQFNQKSVKIKTKLFYKQQKFNLLREENEGYAKLIVELGQDLSGSITSDLILEILKSLIGCFNLDPNRV

Parental  LDVILEVFECRPEHDDFFISLLESYMSMCEPQTLCHILGFKFKFYQEPSGETPSSLYRVAAVLLQFNLID
          LD.ILEVFECRPEH.DFFISLL..YMSMCEPQTLCHILGFKFKFYQEP.GETPSSLYR.AAVLLQFNL.D
Retrocopy LDIILEVFECRPEHHDFFISLLQAYMSMCEPQTLCHILGFKFKFYQEPNGETPSSLYRAAAVLLQFNLLD

Parental  LDDLYVHLLPADNCIMDEYKREIVEAKQIVRKLTMVVLSSEKLDERDKEKDKDDEKVEKPPDNQKLGLLE
          LDDLYVHLLPAD.CIM.EYKREIVEAKQIV.KLTMVVL.SEK.DER.KEK.KDD.KVEK.PDNQKLGLLE
Retrocopy LDDLYVHLLPADSCIMNEYKREIVEAKQIVKKLTMVVLPSEKSDEREKEKKKDD-KVEKAPDNQKLGLLE

Parental  ALLKIGDWQHAQNIMDQMPPYYAASHKLIALAICKLIHITVEPLYRRVGVPKGAKGSPVSALQNKRAPKQ
          ALL.IGDWQHAQ.IMD.MPPYYA.SHK.IALAIC.LIHIT.EP.YRRVGVPKGAKGSPVSALQNK.APKQ
Retrocopy ALLIIGDWQHAQSIMDRMPPYYATSHKVIALAICNLIHITIEPIYRRVGVPKGAKGSPVSALQNKKAPKQ

Parental  VESFEDLRRDVFNMFCYLGPHLSHDPILFAKVVRIGKSFMKEFQSDGSKQEDKEKTEVILSCLLSITDQV
          .ESFEDLRRDVF.MFCYLGPHLSHDPILFAKVVRIGKSFMKEFQSDG.KQE.KEK.E.ILSCLLS.TDQV
Retrocopy AESFEDLRRDVFSMFCYLGPHLSHDPILFAKVVRIGKSFMKEFQSDG-KQENKEKMETILSCLLSVTDQV

Parental  LLPSLSLMDCNACMSEELWGMFKTFPYQHRYRLYGQWKNETYNGHPLLVKVKAQTIDRAKYIMKRLTKEN
          LLPSLSLMDCNACMSEELW.MFKTFPYQHRYRLYGQWKNETYN.HPLLVKVKA.TIDRAKYIMKRLTKEN
Retrocopy LLPSLSLMDCNACMSEELWAMFKTFPYQHRYRLYGQWKNETYNSHPLLVKVKAHTIDRAKYIMKRLTKEN

Parental  VKPSGRQIGKLSHSNPTILFDYILSQIQKYDNLITPVVDSLKYLTSLNYDVLAYCIIEALANPEKERMKH
          VKPSGRQIGKLSHSNPTILFDYILSQIQKYDNLITPVVDSLKYLT.LNYDVLAYCIIEALANPEKERMKH
Retrocopy VKPSGRQIGKLSHSNPTILFDYILSQIQKYDNLITPVVDSLKYLTALNYDVLAYCIIEALANPEKERMKH

Parental  DDTTISSWLQSLASFCGAVFRKYPIDLAGLLQYVANQLKAGKSFDLLILKEVVQKMAGIEITEEMTMEQL
          DDTTIS.WLQSLASFCGAVFRKYPIDLAGLLQYVANQLKAGKSFDLLILKEVVQKMAGIE.TEEMTMEQL
Retrocopy DDTTISNWLQSLASFCGAVFRKYPIDLAGLLQYVANQLKAGKSFDLLILKEVVQKMAGIEVTEEMTMEQL

Parental  EAMTGGEQLKAEGGYFGQIRNTKKSSQRLKDALLDHDLALPLCLLMAQQRNGVIFQEGGEKHLKLVGKLY
          EAMTGGEQLKAEGGYFGQIRNTKKSSQRLKDALLDHDLALPLCLLMAQQRNGVIFQEGGEKHLKLVGKLY
Retrocopy EAMTGGEQLKAEGGYFGQIRNTKKSSQRLKDALLDHDLALPLCLLMAQQRNGVIFQEGGEKHLKLVGKLY

Parental  DQCHDTLVQFGGFLASNLSTEDYIKRVPSIDVLCNEFHTPHDAAFFLSRPMYAHHISSKYDELKKSEKGS
          DQCHDTLVQFGGFLASNLST.DYIKRVPSIDVLCNEFHTPHDAAFFLSRPMYAHHISSKYDELKKSEKGS
Retrocopy DQCHDTLVQFGGFLASNLSTDDYIKRVPSIDVLCNEFHTPHDAAFFLSRPMYAHHISSKYDELKKSEKGS

Parental  KQQHKVHKYITSCEMVMAPVHEAVVSLHVAKVWDDISPQFYATFWSLTMYDLAVPHTSYEREVNKLKVQM
          KQQHKVHKYITSCEMVMAPVHEAVVSLH..KVW.DISPQFY.TFWSLTMYDLAVPHTSYEREVNKLK.QM
Retrocopy KQQHKVHKYITSCEMVMAPVHEAVVSLHISKVWEDISPQFYTTFWSLTMYDLAVPHTSYEREVNKLKIQM

Parental  KAIDDNQEMPPNKKKKEKERCTALQDKLLEEEKKQMEHVQRVLQRLKLEKDNWLLAKSTKNETITKFLQL
          KA.DDNQEMP.NKKKKEKERCTALQDKLLEEEKKQMEHVQRVL.RLKLEKDNWLLAKSTKNETITKFLQL
Retrocopy KAVDDNQEMPLNKKKKEKERCTALQDKLLEEEKKQMEHVQRVLHRLKLEKDNWLLAKSTKNETITKFLQL

Parental  CIFPRCIFSAIDAVYCARFVELVHQQKTPNFSTLLCYDRVFSDIIYTVASCTENEASRYGRFLCCMLETV
          CIFPRCIFSAID.VYCA.FVELVHQQKTPNFSTLLCYDRVFSDIIY.VAS.TENEASRYGRFLCCMLETV
Retrocopy CIFPRCIFSAIDSVYCAHFVELVHQQKTPNFSTLLCYDRVFSDIIYMVASFTENEASRYGRFLCCMLETV

Parental  TRWHSDRATYEKECGNYPGFLTILRATGFDGGNKADQLDYENFRHVVHKWHYKLTKASVHCLETGEYTHI
          TRWHSDR.TYEKECGNYPGFLTILRATGFDGGNKADQLDYENFRHVVHKWHYKLTKASVHCLETGEYTHI
Retrocopy TRWHSDRSTYEKECGNYPGFLTILRATGFDGGNKADQLDYENFRHVVHKWHYKLTKASVHCLETGEYTHI

Parental  RNILIVLTKILPWYPKVLNLGQALERRVNKICQEEKEKRPDLYALAMGYSGQLKSRKSHMIPENEFHHKD
          RNILIVLTKILPWYPKVLNLGQALERRV.KICQEEKEK.PDLYALAM.YSGQLKSRKS.MIPENEFHHKD
Retrocopy RNILIVLTKILPWYPKVLNLGQALERRVHKICQEEKEKKPDLYALAMVYSGQLKSRKSYMIPENEFHHKD

Parental  PPPRNAVASVQ-NGPGGGTSSSSIGSASKSDESGAEETDKSRERSQCGTKAVNKASSTTPKGNSSNGNSG
          PPPRNA..SVQ.NGP..G...SSIGS.SK.DES.AEE.DKSRERSQC..KAVNKASS..PKGN.SNGNSG
Retrocopy PPPRNAATSVQPNGPCSGL-PSSIGSTSKLDESSAEEADKSRERSQCAVKAVNKASSVIPKGNLSNGNSG

Parental  SNSNKAVKENDKEKVKEKEKEKKEKTPATTPEARVLGKESKEKPKEERPNKDDKARETKERTPKSDKEKE
          SN..KAVKENDKEK.KEKEKEKKEK.PA.TPEARVLGK.SKEKPKEE.PNKD.K.RE.KER.PKSDK.KE
Retrocopy SNT-KAVKENDKEKGKEKEKEKKEKAPAVTPEARVLGKDSKEKPKEEQPNKDEKIREAKERMPKSDKDKE

Parental  KFKKEEKAKDEKFKTTVPSVESKSTQEREREKEPSRERDVAKEMKSKENVKGGEKPPVSGSLKSPVPRSD
          K.KKEEKAKDEKF...VP.VESKSTQERE.EKEPSRERD.AKEMKSKENVKGGEK.P.SGSLKSPV.R.D
Retrocopy KLKKEEKAKDEKFRIIVPNVESKSTQEREKEKEPSRERDLAKEMKSKENVKGGEKAPLSGSLKSPVSRTD

Parental  ISEPDREQKRRKIDTHPSPSHSSTVKDSLIDLKDSSAKLYINHNPPPLSKSKEREMDKKDLDKSRERSRE
          I.EP.RE.KRRK.D.HPSPSH.ST.KDSL..LK.SSAKLYINH.PPPL.KSKERE.DKKDLDKSRERSRE
Retrocopy IIEPERE-KRRKVDSHPSPSHASTIKDSLVKLKESSAKLYINHIPPPLCKSKEREADKKDLDKSRERSRE

Parental  REKKDEKDRKERKRDHSNNDREVPPDITKRRKEENGTMGVSKHKSESPCESQYPNEKDKEKNKSKSSGKE
          REKK.EKDRKERKRD.SNNDRE.P.D..KRRK.ENG..GVSKHKSESPCES.YPNEKDKEK.KSKSSGKE
Retrocopy REKKEEKDRKERKRDYSNNDREAPLDLIKRRKDENGILGVSKHKSESPCESLYPNEKDKEKIKSKSSGKE

Parental  KGSSDSFKSEKMDKISSGGKKESRHDKEKIEKKEKRDSSGGKEEKKHHKSSDKHR
          K..SDSFK.EK.DKISS.GKKES.HDKEKIEKKEK.DSSG.KEEKKHHKSSDKHR
Retrocopy K--SDSFKPEKIDKISS-GKKESGHDKEKIEKKEKWDSSGDKEEKKHHKSSDKHR

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	12.51 RPM	42.85 RPM
SRP017611_kidney	6.63 RPM	65.60 RPM
SRP017611_liver	4.64 RPM	38.59 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_89 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_89 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_89 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_172

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000013656	4 retrocopies	retro_mluc_2531, retro_mluc_2546, retro_mluc_2599, retro_mluc_2606,
Mus musculus	ENSMUSG00000037475	1 retrocopy	retro_mmus_172,
Rattus norvegicus	ENSRNOG00000007315	1 retrocopy	retro_rnor_89 ,