RetrogeneDB ID: retro_rnor_1704

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:254976231..254976765(-)
• Located in intron of: ENSRNOG00000011053

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aimp1
• Ensembl ID: ENSRNOG00000011384
• Aliases: Aimp1, Emap2, Scye1
• Description: aminoacyl tRNA synthase complex-interacting multifunctional protein 1 [Source:RefSeq peptide;Acc:NP_446209]

Sequence

>retro_rnor_1704
GAGAAGCATCAGCAGTCGGCGGCAGCAAGTGCTGCCTTGAAGCCTGTCGAGTATCACGCCTGGATCTTCGATCTGGTTCT
GTCCTCACTGCCAAGAAACACCCGGATGCAGATTCATTGTATGTGGGGGAAGTCGATGTGGGAGAAGCAGCCCCACGGAC
GGTCGTCAGCGGGCTGGTTAGTCATGTCCCCCTAGAACAGATGCAAAACCGAATGGTGGTTTTGCTTTGTAATCTGAAGT
CTGCAAAAAATGTGGGGAGTGCTGTCCCAAGCAATGGTGATATGCGCCAGTTCACCAGAGAAAGTGGGGATTCTGGCCCC
TCCCCGTGGGTCTGTTCCTGGAGACAGAATTACTTTTGATGCTTTCCCTGGAGAGCCTGACAAGGAGCTGAACCCTAAGA
AGCAGATCTGGGAGCAGATCCAGCCTGACCTGCACACCAATGACGAATGTGTGGCCATGTACAAAGGAGCTCCCTTTGAG
GTGAAGGGGAAGGGAGTTTGCAGGGCCCAAACCATGGCCAACAGCGGAATTAAA

Alignment

ORF - retro_rnor_1704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.44 %
• Parental protein coverage: 56.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKKQQSAAASADSKPVD-VSRLDLRIGCIVTAKKHPDADSLYVEEVDVGEAAPRTVVSGLVNHVPLEQMQ
          EK.QQSAAASA..KPV..VSRLDLR.G...TAKKHPDADSLYV.EVDVGEAAPRTVVSGLV.HVPLEQMQ
Retrocopy EKHQQSAAASAALKPVE<VSRLDLRSGSVLTAKKHPDADSLYVGEVDVGEAAPRTVVSGLVSHVPLEQMQ

Parental  NRMVVLLCNLKPAK-MRGVLSQAMVMCASSPEKVEILAPPNGSVPGDRITFDAFPGEPDKELNPKKKIWE
          NRMVVLLCNLK.AK.M.GVLSQAMV.CASSPEKV.ILAPP.GSVPGDRITFDAFPGEPDKELNPKK.IWE
Retrocopy NRMVVLLCNLKSAK>MWGVLSQAMVICASSPEKVGILAPPRGSVPGDRITFDAFPGEPDKELNPKKQIWE

Parental  QIQPDLHTNDECVATYKGAPFEVKGKGVCRAQTMANSGIK
          QIQPDLHTNDECVA.YKGAPFEVKGKGVCRAQTMANSGIK
Retrocopy QIQPDLHTNDECVAMYKGAPFEVKGKGVCRAQTMANSGIK

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	26.31 RPM
SRP017611_kidney	0.00 RPM	24.63 RPM
SRP017611_liver	0.07 RPM	11.16 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1704 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1704 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000619	2 retrocopies	retro_chof_1176, retro_chof_2050,
Callithrix jacchus	ENSCJAG00000015885	1 retrocopy	retro_cjac_2504,
Dipodomys ordii	ENSDORG00000005018	1 retrocopy	retro_dord_540,
Mustela putorius furo	ENSMPUG00000008952	1 retrocopy	retro_mputfur_1606,
Mus musculus	ENSMUSG00000028029	2 retrocopies	retro_mmus_2271, retro_mmus_3334,
Pongo abelii	ENSPPYG00000014981	1 retrocopy	retro_pabe_1780,
Rattus norvegicus	ENSRNOG00000011384	1 retrocopy	retro_rnor_1704 ,
Ictidomys tridecemlineatus	ENSSTOG00000008178	1 retrocopy	retro_itri_1173,
Tupaia belangeri	ENSTBEG00000004412	1 retrocopy	retro_tbel_4008,