RetrogeneDB ID: retro_rnor_1140

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:29662707..29663268(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Brix1
• Ensembl ID: ENSRNOG00000018021
• Aliases: Brix1, Bxdc2, RGD1308508
• Description: ribosome biogenesis protein BRX1 homolog [Source:RefSeq peptide;Acc:NP_001025086]

Sequence

>retro_rnor_1140
ATTAACAAGGTTTGTGAAATTAAAAAAAAAAAAACCTGCAATAAATGCATCTATTCTGAAGCTAAGGAAAACCGGATCTC
TATATGTGGCTTTCAAACTCACCACATGAACCACTTGTCAAATTCTTATTTCAAAATGTTCATACCGTGGCTGCGCTAAG
GATGACTGGAAACCGTTTGAGAAGCCCTTGCCCCCGTTTGTATCTTAGCCCTGCTTTTGATGAGTTGCCACATGGCACTT
GGTTAAAAGAACTCTTAATTCAGATCCTTTGTGACCGCCTCATTCTTCCAAGAGTCAGCTGTCCGTGGACGTGTTTACTT
CCACCATTTTGGATTACAGGTTATGGTTTTAGAACCTCCAGATTATAGAAGAAGATATGGCTATGGTGGAAACGGGACTT
CATTTTGTCTTCAGTGTCACCAAGTTTTTTCAGGGAAGGTTTGGAGGACCAACTTCATAAGAAAATCCTCGTTATCAGCC
TTCACGCTAGTACCAGCATGTCTAAAGCCCATCACAGCTTCAAAATACTGAGAGAAACAGGGGATCCATGGTGTTCAGAA
A

Alignment

ORF - retro_rnor_1140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 52.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  INEVCEMKN---CNKCIYFEAKK-KQDLYMWLSNSPHGPSAKFLVQNIHTLAELKMTGNCLKGSRPLLSF
          IN.VCE......CNKCIY.EAK..K.DLYMWLSNSPH.P..KFL.QN.HT.A.L.MTGN.L....P.L..
Retrocopy INKVCEIXXXXXCNKCIYSEAKE<KPDLYMWLSNSPHEPLVKFLFQNVHTVAALRMTGNRLRSPCPRLYL

Parental  DPAFDDLPHYALLKEFLIQIFST-PRYHPKSQPFVDHVFTFTILDNRIWFRNFQIIEEDAALVEIGPRFV
          .PAFD.LPH...LKE.LIQI....P....KSQ..VD.VFT.TILD.R.WF.N.QIIEED.A.VE.G..FV
Retrocopy SPAFDELPHGTWLKELLIQILCD<PPHSSKSQLSVD-VFTSTILDYRLWF*NLQIIEEDMAMVETGLHFV

Parental  LNLIKIFQGSFGGPTLYENPHYQSPNMHRRV-VRSITAAKYREKQQVKDVQK
          ....K.FQG.FGGPT..ENP.YQ.......V....ITA.KY.EKQ....VQK
Retrocopy FSVTKFFQGRFGGPTS*ENPRYQPSR*YQHV<LKPITASKY*EKQGIHGVQK

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	23.15 RPM
SRP017611_kidney	0.00 RPM	17.93 RPM
SRP017611_liver	0.00 RPM	8.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1140 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1140 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001790	2 retrocopies	retro_chof_1664, retro_chof_1776,
Callithrix jacchus	ENSCJAG00000018506	1 retrocopy	retro_cjac_1389,
Homo sapiens	ENSG00000113460	1 retrocopy	retro_hsap_3954,
Gorilla gorilla	ENSGGOG00000004225	1 retrocopy	retro_ggor_2657,
Loxodonta africana	ENSLAFG00000007249	1 retrocopy	retro_lafr_1116,
Myotis lucifugus	ENSMLUG00000029255	3 retrocopies	retro_mluc_1402, retro_mluc_707, retro_mluc_963,
Macaca mulatta	ENSMMUG00000000442	1 retrocopy	retro_mmul_2289,
Monodelphis domestica	ENSMODG00000020386	1 retrocopy	retro_mdom_1032,
Nomascus leucogenys	ENSNLEG00000014452	1 retrocopy	retro_nleu_533,
Otolemur garnettii	ENSOGAG00000014827	2 retrocopies	retro_ogar_3116, retro_ogar_793,
Pongo abelii	ENSPPYG00000015390	2 retrocopies	retro_pabe_3258, retro_pabe_3379,
Pan troglodytes	ENSPTRG00000016784	1 retrocopy	retro_ptro_2684,
Rattus norvegicus	ENSRNOG00000018021	1 retrocopy	retro_rnor_1140 ,
Tupaia belangeri	ENSTBEG00000011652	9 retrocopies	retro_tbel_1963, retro_tbel_1964, retro_tbel_2981, retro_tbel_3002, retro_tbel_3082, retro_tbel_4194, retro_tbel_4229, retro_tbel_4418, retro_tbel_954,