RetrogeneDB ID: retro_rnor_2971

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:116299493..116300366(-)
• Located in intron of: ENSRNOG00000019429

Retrocopy information

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

Parental gene information

• Parental gene symbol: Apex1
• Ensembl ID: ENSRNOG00000009663
• Aliases: Apex1, APE, Apex, REF-1
• Description: DNA-(apurinic or apyrimidinic site) lyase DNA-(apurinic or apyrimidinic site) lyase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P43138]

Sequence

>retro_rnor_2971
GAACAACCCAAGTCAGAGCCAGAGACCAAGAAGAGTAAGGGGGCGGCAAAGAAAACTGTCCTGCATGAGGGCCCTCCGGA
TCAGAAAACCTCACAGTGGCCAATCCGCCACACTCAGATAAGCTCCTGGGAAGTGGGTGGGCTTCCAGCCTGCATTCAAA
AGAAAGGTTTGGACTGTGTGAAGGAAGAAACACCAGACATTTTGTGCCTTCAAGAGACCAAATGCTCAAAGAACAAACTC
CTGGCTGAACTGCAGGAGCTGCCTGGACTCACCCGTCAGTACTGGTCAGCTCCATCAGACACAGAAGCATACAGTGGTGT
GGGCCTACTCTCCACCAGTGCCCACTCAAAGTCCCTTCTGGCATTTATAGGTGAGGCAGAACATGATCAGGAAGACCGGT
GATTGTGGCTGAACTGGCCTCCTGTGTAATAACCTATGTTCCCAACGCAGGCAGGAGTTTGGTAAGACTGGAGTACCAGC
AGTGCTGGGATGAAGCCTTTTGCAAGTTTCTAAAGGACTTGGCTTCCTGAAAACCTCTGGTACTGTGTGGGAATCTCAAT
GTGACTCATGAAGAAATCTACCTTTGTAACCCCAAAGGAAACAAAAAGAATGCTGATTTTACTCCCCAGGAGCGCCAGGG
CTTTGGGGAATTGCTACAGGCGGTACCACTGGCTGACAACCTCCGGCATCTCTACCCCAACACAGTCTACGCTTAGACTT
TCTGGACTACATGATGGATGCCCACCCAAGAACATCAGTTGGCACCTTGATTAGTTTTTGCTATCCTACTCTTTTTTTTA
CCTGCATTATGACAGCAAGATTTGGTCCAAGGTTCTTGACAGTGACCACTGTCCCATCACCCTTTGCCTAGCA

Alignment

ORF - retro_rnor_2971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.33 %
• Parental protein coverage: 93.38 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ETKKSKGAAKKTEKEAAGEGPVLYEDPPDQKTSASGKSATLKICSWNVDGLRAWIKKKGLDWVKEEAPDI
          E..KS....KK.....A....VL.E.PPDQKTS......T..I.SW.V.GL.A.I.KKGLD.VKEE.PDI
Retrocopy EQPKSEPETKKSK--GAAKKTVLHEGPPDQKTSQWPIRHT-QISSWEVGGLPACIQKKGLDCVKEETPDI

Parental  LCLQETKCSENKLPAELQELPGLTHQYWSAPSDKEGYSGVGLLS-RQCPLKVSYGIGEEEHDQEGR-VIV
          LCLQETKCS.NKL.AELQELPGLT.QYWSAPSD.E.YSGVGLLS..QCPLKV..GI........GR.VIV
Retrocopy LCLQETKCSKNKLLAELQELPGLTRQYWSAPSDTEAYSGVGLLS<HQCPLKVPSGIYR*GRT*SGRPVIV

Parental  AEFESFILVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEIDLRNPKGNKKN
          AE..S......YVPNAGR.LVRLEY.Q.WDEAF.KFLKDLAS.KPLVLCG.LNV.HEEI.L.NPKGNKKN
Retrocopy AELASCVI--TYVPNAGRSLVRLEYQQCWDEAFCKFLKDLAS*KPLVLCGNLNVTHEEIYLCNPKGNKKN

Parental  AGFTPQERQGFGEMLQAVPLADSFRHLYPNTAYAYTFWT-YMMNAR-SKNVGWRLDYFLLSHSLLPALCD
          A.FTPQERQGFGE.LQAVPLAD..RHLYPNT.YA.TFWT.YMM.A...KN..W.LD.FLLS........D
Retrocopy ADFTPQERQGFGELLQAVPLADNLRHLYPNTVYA*TFWT<YMMDAH<PKNISWHLD*FLLSYXXXXLHYD

Parental  SKIRSKALGSDHCPITLYLA
          SKI.SK.L.SDHCPITL.LA
Retrocopy SKIWSKVLDSDHCPITLCLA

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	33.29 RPM
SRP017611_kidney	0.07 RPM	31.96 RPM
SRP017611_liver	0.13 RPM	7.93 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2971 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2971 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002745	1 retrocopy	retro_btau_1729,
Echinops telfairi	ENSETEG00000004855	1 retrocopy	retro_etel_1392,
Loxodonta africana	ENSLAFG00000021872	1 retrocopy	retro_lafr_948,
Mus musculus	ENSMUSG00000035960	2 retrocopies	retro_mmus_2027, retro_mmus_433,
Otolemur garnettii	ENSOGAG00000013335	3 retrocopies	retro_ogar_1284, retro_ogar_2145, retro_ogar_3243,
Rattus norvegicus	ENSRNOG00000000166	1 retrocopy	retro_rnor_1061,
Rattus norvegicus	ENSRNOG00000009663	1 retrocopy	retro_rnor_2971 ,
Ictidomys tridecemlineatus	ENSSTOG00000010096	1 retrocopy	retro_itri_1560,
Tupaia belangeri	ENSTBEG00000006405	1 retrocopy	retro_tbel_3409,