RetrogeneDB ID: retro_rnor_2324

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:122807651..122808300(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aimp2
• Ensembl ID: ENSRNOG00000001044
• Aliases: Aimp2, Jtv1
• Description: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q32PX2]

Sequence

>retro_rnor_2324
ATGTAGATGTACCAGGTAAAGCCCTATCATGGAGGCAGCACACCTCTGTGTGTAGAGTTTCCAACCTGCATGTACCGGCC
ACCCAATGTGCACAGGAAGACCACCAGTCCCGCGACCGACGCGGGGCCAAGTGCAGGAAACATTTGAGCCATCTTTGCGA
GCCCTTGAATCTCGGCAGGATGATATTTTAAAGCGCTTGTATGAGTTGAAGGCAGCAGTCGATGGCCTTTCAAAGATGAT
TCACACCCCAGCTGCGGACTTGGACTTAACCAACATCCTGCAAGCTGACAAGCCCACGACATTAACCACAAATGCATTGG
ACTTGTATTGTGTGCTTGGAAAGGATTATGGGGCGCTGAAAGACATCGTGATCAAAGCAAACCCAGCCTCCCCACCCCTG
TTCCTATTTGTACTGCACAGGCTGCTCTGTGAATGCTACAGGGTTCTGTCCACAACACACACATATTCGTCTGTTAAGAA
TGTACCTGAGAATCTTCTCAAGTGCTTCGGGGAGCAGGCTGGAAAACAGTCCCACAATGGCTATCAGCTGGGCTTCGCTC
TGATTTGGAAGAATGTGCCCAAGACATAGGTGAAGTTCACTGTAGAAACAATGTGCCCCATCGAAGGAGAGGGGAACATC
GCACGTTTC

Alignment

ORF - retro_rnor_2324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.18 %
• Parental protein coverage: 67.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPMYQVKPYHGGSAPLRVELPTCMYRLPNVHSKTTSPATDAG-HVQEPSEPSLRALESRQDDILKRLYEL
          M.MYQVKPYHGGS.PL.VE.PTCMYR.PNVH.KTTSPATDAG..VQE..EPSLRALESRQDDILKRLYEL
Retrocopy M*MYQVKPYHGGSTPLCVEFPTCMYRPPNVHRKTTSPATDAG>QVQETFEPSLRALESRQDDILKRLYEL

Parental  KAAVDGLSKMIHTPDADLDVTNILQADEPTTLTTNALDLNSVLGKDYGALKDIVINANPASPPLSLLVLH
          KAAVDGLSKMIHTP.ADLD.TNILQAD.PTTLTTNALDL..VLGKDYGALKDIVI.ANPASPPL.L.VLH
Retrocopy KAAVDGLSKMIHTPAADLDLTNILQADKPTTLTTNALDLYCVLGKDYGALKDIVIKANPASPPLFLFVLH

Parental  RLLCERYRVLSTVHTHSSVKNVPENLLKCFGEQARKQSRHEYQLGFTLIWKNVPKTQMKFSVQTMCPIEG
          RLLCE.YRVLST.HT.SSVKNVPENLLKCFGEQA.KQS...YQLGF.LIWKNVPKT..KF.V.TMCPIEG
Retrocopy RLLCECYRVLSTTHTYSSVKNVPENLLKCFGEQAGKQSHNGYQLGFALIWKNVPKT*VKFTVETMCPIEG

Parental  EGNIARF
          EGNIARF
Retrocopy EGNIARF

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	15.96 RPM
SRP017611_kidney	0.00 RPM	21.77 RPM
SRP017611_liver	0.00 RPM	6.05 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2324 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2324 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000016092	1 retrocopy	retro_pvam_27,
Rattus norvegicus	ENSRNOG00000001044	1 retrocopy	retro_rnor_2324 ,
Ictidomys tridecemlineatus	ENSSTOG00000029156	1 retrocopy	retro_itri_923,