RetrogeneDB ID: retro_rnor_1411

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:83848477..83849517(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tp53
• Ensembl ID: ENSRNOG00000010756
• Aliases: Tp53, Trp53, p53
• Description: Cellular tumor antigen p53 [Source:UniProtKB/Swiss-Prot;Acc:P10361]

Sequence

>retro_rnor_1411
GAGGATTCATATTCGGATATCAGTATGGAGCTCACTCTGAGTCAGGAGAAAATTTCAGATTTGTGAAAACTACTCCCTCT
GGAAGATATTCTGTCCACTGTAGCAGTGTCACCTAATTCCACAGAAGATCTGTTCCTGTCCCAGGACGTTGCAGAGTTGT
AGAAGGCCAAGAGGAAGACCTCCAAGTGTCAGCTCCTGCAGCAAAGGAGCCTGGAACTGAGGCCTCTGCACCCACTGCCC
CTGCTCTAGTCACTCCATGGCCCTGTTACCTTCTGTCCCTTCTCAAAAAAACCTTACCAAGGCAATTATGCCTTCTACCT
GGGGTTCCTGCAGTCAGAGACAGCCAAGTTTGTTATGTGCATGTACTCCACTTCCCTCAATACTCTATTCTGCCAGCTGG
CGAAGACATGGTCCTGTACAGTTGTGGGTCAGCTCCATACCTCCAGCTGGTACCCATGTCCGTGCCATGGCCATCTAGAA
GAAGTCACAATCCTTGACTGAGGTTGTGAGACACTGCCCCCATCATGAGCGTTGCTCCAGTGGTGATGGCCTGGCTCCTT
CCCAGCCTCTTATCTGGGTGGAAGGAAATTTGTATGCTGAGCATCTGGACAGCAGGTAGACTTTTGGACACAGTGTGGTG
GTACCATATGAGCCACCTGAGGTCTGTTCTGACTATACCACCATCCACTACAAGTCCATGTGTAATAGTTCCTACATGGG
GGACATGACCTGCCTGCCCATCCTTACCATCACCACATTGGAAGATTCCAGTGGAAACCTTCCAGGACAGGACAGCTTTG
AAGTTCATGTTTGTGCCTGTCCTGGGAGAGACCATGGGTCAGAGGAAGAAAATTTCCACAAAAAGAAAGAACATTGCCTA
GGACTGCCCCCGGGAAATGCTAAGAGAGCACTGCCTACCAGCACAAGCTCCTCTCCCCGACAACAGAAAAAAAAAACTTG
ATAGAGAATATTTCACCCTTAAGGTCCGCCGGCATGTGCGCTTCGAGATGTTCGGAGAGCTGAATGAGGCAACAGGGCTC

Alignment

ORF - retro_rnor_1411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.5 %
• Parental protein coverage: 88.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EDSQSDMSIELPLSQETFSCLWKLLPPDDILPTTATGSPNSMEDLFLPQDVAEL-LEGPEEALQVSAPAA
          EDS.SD.S.EL.LSQE..S.L.KLLP..DIL.T.A..SPNS.EDLFL.QDVAEL..EG.EE.LQVSAPAA
Retrocopy EDSYSDISMELTLSQEKISDL*KLLPLEDILSTVAV-SPNSTEDLFLSQDVAEL<VEGQEEDLQVSAPAA

Parental  QEPGTEAPAPVAPASATPW-PLSSSVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSISLNKLFCQLAKTC
          .EPGTEA.AP.APA..TPW.P......S.K.YQGNY.F.LGFLQS.TAK.VMC.YS.SLN.LFCQLAKT.
Retrocopy KEPGTEASAPTAPALVTPW>PVTFCPFSKKPYQGNYAFYLGFLQSETAKFVMCMYSTSLNTLFCQLAKTW

Parental  -PVQLWVTSTPPPGTRVRAMAIYKKSQHMTEVVRRCPHHERCSDGDGLAPPQHLIRVEGNPYAEYLDDRQ
          .PVQLWV.S.PP.GT.VRAMAI.KKSQ..TEVVR.CPHHERCS.GDGLAP.Q.LI.VEGN.YAE.LD.R.
Retrocopy >PVQLWVSSIPPAGTHVRAMAI*KKSQSLTEVVRHCPHHERCSSGDGLAPSQPLIWVEGNLYAEHLDSR*

Parental  TFRHSVVVPYEPPEVGSDYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGR
          TF.HSVVVPYEPPEV.SDYTTIHYK.MCNSS.MG.M...PILTI.TLEDSSGNL.G.DSFEV.VCACPGR
Retrocopy TFGHSVVVPYEPPEVCSDYTTIHYKSMCNSSYMGDMTCLPILTITTLEDSSGNLPGQDSFEVHVCACPGR

Parental  DRRTEEENFRKKEEHCPELPPGSAKRALPTSTSSSPQQK-KKPLDGEYFTLKIRGRERFEMFRELNEALE
          D...EEENF.KK.EHC..LPPG.AKRALPTSTSSSP.Q.....LD.EYFTLK.R...RFEMF.ELNEA..
Retrocopy DHGSEEENFHKKKEHCLGLPPGNAKRALPTSTSSSPRQQ>XXXLDREYFTLKVRRHVRFEMFGELNEATG

Parental  L
          L
Retrocopy L

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	16.82 RPM
SRP017611_kidney	0.00 RPM	37.61 RPM
SRP017611_liver	0.00 RPM	26.76 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1411 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1411 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013135	2 retrocopies	retro_meug_1464, retro_meug_599,
Myotis lucifugus	ENSMLUG00000006411	3 retrocopies	retro_mluc_2049, retro_mluc_2050, retro_mluc_452,
Monodelphis domestica	ENSMODG00000007271	1 retrocopy	retro_mdom_372,
Rattus norvegicus	ENSRNOG00000010756	1 retrocopy	retro_rnor_1411 ,
Sarcophilus harrisii	ENSSHAG00000015510	1 retrocopy	retro_shar_250,