RetrogeneDB ID: retro_rnor_1061

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:71740227..71741772(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000026046
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Apex2
• Ensembl ID: ENSRNOG00000000166
• Aliases: None
• Description: None

Sequence

>retro_rnor_1061
ATGTTGCGCGTGGTAAGCTGGAACATCAATGGGATCCGGAGACCCCTGCAAGGTCTGGGATGCGAGGTAACCAGCAACTG
TCCCACAGCCTTGAGACATATTTTAAGGGAACTGGATGCCGATATAGTCTGTCTCCAGGAGACCAAAGTGAGCAGAGATG
CGCTGACAGAGCCCCTGGCTGTTGTTGAGGGCTATAACTCCTATTTCAGCTTCAGCCGCAGCCGGAGTGGCTATTCTGGT
GTAGCTACTTTCTGTAAGGACAGTGTTACACCAGTGGCTGCTGAAGAAGGCCTGAGTGGTCAGTTTGCCACCCTGAGTGG
GCATGTCGGTTGCTATGGAAACATGAACGAGTTCACCCAAGAGCAACTCCGGGCTCTGGATAGCGAGGGCCGGGCTCTCC
TTACACAGCACAAGATCTGTACACAGGAAGGGAAGGAGAAGCCTTTGACCCTGATCAATGTGTACTGCCCGCATGCCAGT
CCTGGGAACCATGAGCGGCTGACCTTTAAGATGCGTTTCTATCGCCTGCTGCAGATCCGAGCAGAAGCACTCCTGGCAGC
CGGAAGTCATGTGATAATCCTGGGGGACATAAATACAGCCCACCATCCCATTGACCACTGTAATGCTGGCAATCTGGAGT
GCTTTGAAGAAGACCTGGGACGTAGATGGATGGATGGCTTGCTCAGTAACCTGGAATACCCGGCTGGGTCCCATATAGGG
CCTTTCATGGATAGCTACCGCTATTTCTATCCAAAACAGGAGAGGGCCTTCACCTGCTGGTCAATGATCAGTGGGGCACG
CAGTCTCAACTATGGTACCCGACTTGACTACATCCTAGGAAACAGGGATCTAATTATAGACACTTTACAAGATGCCTTTC
TGCTCCCCGAGGTGATGGGCTCTGACCACTGCCCTGTGGGAGCTGTCTTGAATGTGTCCTGTGTGCCAGCGAAACAGTGT
CCAGCTCTGTGCACCCGTTTCCTTCCCGAGTTTGCAGGTACCCAGCTCAAGATTCTTGGCTTCCTGGTCCCTTGTGAACA
AGAACCTATGTGCGGGCAGTCAGTCCTGCAGTCCAGCAAACAAATCCAACCACAGAAACAAAGAAAATCTCAAGCCCATA
GGCATTCATCCAGGCCTCGAAAGCCTGGTTCCAGAAGACCCCAGAAAAACCTGAGGAGCTATTTTCAGCCTTCTGTTAGC
CTTTCCCAGACTTCTCCTGCTGTGGAACTGCCTCAGCTGCCTCTAGTGGGCACTCTCGTAACTCCAACAACTCTGGAAGG
GGATGTGATAGCCACAGGGACCGATAAGCAGGTCAAGGTTTCTGAGGTCAGAGATGAGGAGGAGGCACAGGCCTCATTCT
GGAAGTCCGTGCTGAGTGGGCCATCACCAATGCCCCTCTGTGGAGGCCACAGGGAGCCGTGTGTGATGCGGATCGTGAAA
AAACCAGGACCTAATCTGGGTCGCCATTTCTACACATGTGCCAAGCCACAAGGTCCTCCAAATGATCTCTCATCAAGCTG
CAACTTCTTCCTGTGGAGCAAGCCC

Alignment

ORF - retro_rnor_1061 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.21 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRVVSWNINGIRSPLQGLAGQEPSNSPTALRRVLDELDADIVCLQETKVTRDVLTEPLAIVEGYNSYFS
          MLRVVSWNINGIR.PLQGL.....SN.PTALR..L.ELDADIVCLQETKV.RD.LTEPLA.VEGYNSYFS
Retrocopy MLRVVSWNINGIRRPLQGLGCEVTSNCPTALRHILRELDADIVCLQETKVSRDALTEPLAVVEGYNSYFS

Parental  FSRSRSGYSGVATFCKDSATPVAAEEGLSGVFATLNGDIGCYGNTDEFTQEELRVLDSEGRAFLTQHKIR
          FSRSRSGYSGVATFCKDS.TPVAAEEGLSG.FATL.G..GCYGN..EFTQE.LR.LDSEGRA.LTQHKI.
Retrocopy FSRSRSGYSGVATFCKDSVTPVAAEEGLSGQFATLSGHVGCYGNMNEFTQEQLRALDSEGRALLTQHKIC

Parental  TLEGKEKTLTLINVYCPHADPGKPERLTFKMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHCDAS
          T.EGKEK.LTLINVYCPHA.PG..ERLTFKMRFYRLLQIRAEALLAAGSHVIILGD.NTAH.PIDHC.A.
Retrocopy TQEGKEKPLTLINVYCPHASPGNHERLTFKMRFYRLLQIRAEALLAAGSHVIILGDINTAHHPIDHCNAG

Parental  SLECFEEDPGRKWMDGLLSNPGNEAGPHIGHFMDSFRYFHPKQQRAFTCWSVVSGARHLNYGSRLDYVLG
          .LECFEED.GR.WMDGLLSN....AG.HIG.FMDS.RYF.PKQ.RAFTCWS..SGAR.LNYG.RLDY.LG
Retrocopy NLECFEEDLGRRWMDGLLSNLEYPAGSHIGPFMDSYRYFYPKQERAFTCWSMISGARSLNYGTRLDYILG

Parental  DRSLVIDTFQASFLLPEVMGSDHCPVGAVLNVSCVPAKQCPALCTRFLPEFAGTQLKILRFLVPLEQEPV
          .R.L.IDT.Q..FLLPEVMGSDHCPVGAVLNVSCVPAKQCPALCTRFLPEFAGTQLKIL.FLVP.EQEP.
Retrocopy NRDLIIDTLQDAFLLPEVMGSDHCPVGAVLNVSCVPAKQCPALCTRFLPEFAGTQLKILGFLVPCEQEPM

Parental  KEQPVLQ-PHQIQAQKQ-PSKARIHSTRLRKTQGVPKRNQKSLMSYFQPSSNLSQTSD-VELPTLPLVSP
          ..Q.VLQ...QIQ.QKQ..S.A..HS.R.RK......R.QK.L.SYFQPS..LSQTS..VELP.LPLV..
Retrocopy CGQSVLQSSKQIQPQKQRKSQAHRHSSRPRKPGS--RRPQKNLRSYFQPSVSLSQTSPAVELPQLPLVGT

Parental  LTSTKTAEEVAMATVVKEKNKVPEAKDEKEVRTAFWKSMLSGPSPMPLCGGHREPCVMRTVKKAGPNFGR
          L....T.E....AT......KV.E..DE.E....FWKS.LSGPSPMPLCGGHREPCVMR.VKK.GPN.GR
Retrocopy LVTPTTLEGDVIATGTDKQVKVSEVRDEEEAQASFWKSVLSGPSPMPLCGGHREPCVMRIVKKPGPNLGR

Parental  HFYMCARPRGPPSDPSSRCNFFLWSRP
          HFY.CA.P.GPP.D.SS.CNFFLWS.P
Retrocopy HFYTCAKPQGPPNDLSSSCNFFLWSKP

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	3.31 RPM
SRP017611_kidney	0.00 RPM	4.81 RPM
SRP017611_liver	0.00 RPM	4.91 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1061 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016584	1 retrocopy	retro_cjac_2967,
Myotis lucifugus	ENSMLUG00000016298	1 retrocopy	retro_mluc_287,
Mus musculus	ENSMUSG00000025269	1 retrocopy	retro_mmus_2564,
Rattus norvegicus	ENSRNOG00000000166	1 retrocopy	retro_rnor_1061 ,
Rattus norvegicus	ENSRNOG00000009663	1 retrocopy	retro_rnor_2971,