RetrogeneDB ID: retro_rnor_1055

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:61879309..61880108(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Acat3
• Ensembl ID: ENSRNOG00000019189
• Aliases: None
• Description: acetyl-CoA acetyltransferase, cytosolic [Source:RefSeq peptide;Acc:NP_001006996]

Sequence

>retro_rnor_1055
ATGAATGCAGGCTCATACCCCGTGGTCATCATCTCAGTGGTGCGGACCGCCATAGGTTCCTTCAATGGTGCCCTGTCCAC
CATGCCTGTCCACAACTTGGGGACAATTGTCATCAAAGAAGTCCTTCAGAGGGCCAAGGTGGCTCCAGAAGTGGTATCCG
AGGTCAAATTTGGACACGTTTTGATGGCAGGTTATGGGCAGAATCCTACTCGGCAAGCCAGTGTGGGTGCAGGGATCCCC
TACTCCGTGCCAGCATGGAGCTACCAGATGATCTGTGGCTGGGGCATAAAAACTGTGTGCCTTGCAGCTCAGTCCATAGC
CATGGGTGACTCCACCATTGTGGTTGCTGGAGGCGTGGAGAACATGAGCAATGCTCCTCCCTTGGCTCACCTGAGATCAG
GAGTCAAGATGGGTGAGGTGCCACTCGCTGACAGGATACTCTGTGATGGTCTTACAGATGCATTTCACAACTACCACATG
GGCATCACAGCTGAAAACGTAGCCAAAAAGTGGCAAGTAAGCAGAGAGGCCCAGGACAAGGTTGCAGTTGTGTCCTAGAA
TAGGGCAGAGCATGCGCAGAAAGCTGGCCACTTTGACAAGGAGATTGTGCCAGTGCTAGTGTCTTCTAGAAAAGGTCTTA
CTGAAGTGTAAATCAGTGAGTTTCCTCATCATGGGAATAACCTTGAAGCCATGGTCAAGCTGAAACCTTACTTTCTTACT
GATGGGACTGGAAAAGTCCCCAACGAACGCATCAGGAATGAAACATGGTGCTGCTGCTGTGGTTCTTATGAAGAAGACG

Alignment

ORF - retro_rnor_1055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.94 %
• Parental protein coverage: 67.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNAGSDPVVIISAARTAIGSFNGALSTVPVHNLGTTVIKEVLQRAKVAPEEVSEVIFGHVLTAGCGQNPT
          MNAGS.PVVIIS..RTAIGSFNGALST.PVHNLGT.VIKEVLQRAKVAPE.VSEV.FGHVL.AG.GQNPT
Retrocopy MNAGSYPVVIISVVRTAIGSFNGALSTMPVHNLGTIVIKEVLQRAKVAPEVVSEVKFGHVLMAGYGQNPT

Parental  RQASVGAGIPYSVPAWSCQMICGSGLKAVCLAAQSIAMGDSTIVVAGGMENMSKAPHLAHLRSGVKMGEV
          RQASVGAGIPYSVPAWS.QMICG.G.K.VCLAAQSIAMGDSTIVVAGG.ENMS.AP.LAHLRSGVKMGEV
Retrocopy RQASVGAGIPYSVPAWSYQMICGWGIKTVCLAAQSIAMGDSTIVVAGGVENMSNAPPLAHLRSGVKMGEV

Parental  PLADSILCDGLTDAFHNYHMGITAENVAKKWQVSREAQDKVAVVSQNRAEHAQKAGHFDKEIVPVHVSSR
          PLAD.ILCDGLTDAFHNYHMGITAENVAKKWQVSREAQDKVAVVS.NRAEHAQKAGHFDKEIVPV.VSSR
Retrocopy PLADRILCDGLTDAFHNYHMGITAENVAKKWQVSREAQDKVAVVS*NRAEHAQKAGHFDKEIVPVLVSSR

Parental  KGLTEVKIDEFPRHGSNLEAMSKLKPY-FLTDGTGTVTPANASGMNDGAAAVVLMKKT
          KGLTEV.I.EFP.HG.NLEAM.KLKPY.FL..G.....P.NASGM..GAAAVVLMKKT
Retrocopy KGLTEV*ISEFPHHGNNLEAMVKLKPY>FLLMGLEK-SPTNASGMKHGAAAVVLMKKT

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	13.66 RPM
SRP017611_kidney	0.07 RPM	9.49 RPM
SRP017611_liver	0.00 RPM	13.18 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1055 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002827	1 retrocopy	retro_btau_560,
Callithrix jacchus	ENSCJAG00000011777	1 retrocopy	retro_cjac_1372,
Dasypus novemcinctus	ENSDNOG00000002502	1 retrocopy	retro_dnov_331,
Macaca mulatta	ENSMMUG00000012843	1 retrocopy	retro_mmul_277,
Monodelphis domestica	ENSMODG00000007156	1 retrocopy	retro_mdom_1493,
Rattus norvegicus	ENSRNOG00000019189	1 retrocopy	retro_rnor_1055 ,
Xenopus tropicalis	ENSXETG00000021174	1 retrocopy	retro_xtro_45,