RetrogeneDB ID: retro_rnor_1586

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:260770736..260771540(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pacsin3
• Ensembl ID: ENSRNOG00000014204
• Aliases: Pacsin3, SdpIII
• Description: protein kinase C and casein kinase substrate in neurons 3 [Source:RefSeq peptide;Acc:NP_001009966]

Sequence

>retro_rnor_1586
ATGGTTCCAGAAGAGGACACTGGAGGGGAGGTCCTTAGGGGCAGTTTCTGGGAGGCTGGCAACTACAGAGGACCGTGCAG
AGAGTTGAGGATGGGAACAGGCTGTGTGGGGACCTGGTTGGCTGCTTCCAAGAATGTGCCCACATTGAGAAGACCTATGT
CCAGCAGCTGGTTGACTGGGGCCGCAAATGGAGAAGTGCTGTCAAGAAGGAACCACCATACGGCACTCTGGAGATGGCCT
GGCACGCCTTCTTCACTGAGGCTGAGCGGCCGAGCGAGCTGCACTTGTAGGTGAGGAAGTTGCATGGTCCAGGCAACAAG
TGAGTGAGGACGTGGCAGCGCCTGCCTTTCCACCCGCCAGTGCTGGGGGTTTTCGGGAAAGCCGGGATGCACAGGATGGT
TTCCTTCAGGCCCAGAAGCCCTGGTTAAAGAGGCTGAAGGAGGTTGAAGCTTCTAAGAGCTACCACACAGCCCGCAAGGA
CGAAAAGACAGCCCAGATCTGGGAGAGCCACGTGAAGGCAGACAGCTCCATTTCCCAGGAGCAGCTTGGAAAATTACAGG
AGCAGGTGGGACGCTGCACCAGTGAGGCAGGGAAGATGAAAACCCAGTATGAACAGACCCTGGCAGAGTTAAATTGCTAT
ACCTTATGCTACATGGAGGACATGGAGCAGGCCTTTGAGAACTGCCAGGCTGCTGAGCACCAGCGGCTTACGCTCTTCAA
CGATGTGTTGCTCACCTCGCACCAACACCTCGACCTCTCCTGTAGTGGTAAGTTCCATGGTGCCAGGGCCAGCTGCAGAG
AGGC

Alignment

ORF - retro_rnor_1586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.1 %
• Parental protein coverage: 63.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAPEEDAGGEVLGGSFWEAGNYR-RTVQRVEDGHRLCGDLISCFQERARIEKAYAQQLADWARKWRGAVE
          M.PEED.GGEVL.GSFWEAGNYR.RTVQRVEDG.RLCGDL..CFQE.A.IEK.Y.QQL.DW.RKWR.AV.
Retrocopy MVPEEDTGGEVLRGSFWEAGNYR<RTVQRVEDGNRLCGDLVGCFQECAHIEKTYVQQLVDWGRKWRSAVK

Parental  KGPQYGTLEKAWHAFFTAAERLSELHLEVREKLHGPDSERVRTWQRGAFHRPVLG-GFRESRAAEDGFRK
          K.P.YGTLE.AWHAFFT.AER.SELHL.VR.KLHGP....VRTWQR..FH.PVLG.GFRESR.A.DGF..
Retrocopy KEPPYGTLEMAWHAFFTEAERPSELHL*VR-KLHGPGNK*VRTWQRLPFHPPVLG<GFRESRDAQDGFLQ

Parental  AQKPWLKRLKEVEASKKSYHTARKDEKTAQTRESHAKADSSMSQEQLRKLQERVGRCTKEAEKMKTQYEQ
          AQKPWLKRLKEVEAS.KSYHTARKDEKTAQ..ESH.KADSS.SQEQL.KLQE.VGRCT.EA.KMKTQYEQ
Retrocopy AQKPWLKRLKEVEAS-KSYHTARKDEKTAQIWESHVKADSSISQEQLGKLQEQVGRCTSEAGKMKTQYEQ

Parental  TLAELNRYTPRYMEDMEQAFESCQAAERQRLLFFKDVLLTLHQHLDLSSSDKFHELHR-DLQRG
          TLAELN.YT..YMEDMEQAFE.CQAAE.QRL..F.DVLLT.HQHLDLS.S.KFH......LQRG
Retrocopy TLAELNCYTLCYMEDMEQAFENCQAAEHQRLTLFNDVLLTSHQHLDLSCSGKFHGARA<QLQRG

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	22.79 RPM
SRP017611_kidney	0.00 RPM	13.68 RPM
SRP017611_liver	0.00 RPM	34.83 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1586 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1586 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000009756	2 retrocopies	retro_rnor_1788, retro_rnor_1789,
Rattus norvegicus	ENSRNOG00000014204	1 retrocopy	retro_rnor_1586 ,