RetrogeneDB ID: retro_rnor_1214

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:17765627..17766629(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Prpf31
• Ensembl ID: ENSRNOG00000013504
• Aliases: None
• Description: U4/U6 small nuclear ribonucleoprotein Prp31 [Source:RefSeq peptide;Acc:NP_001099689]

Sequence

>retro_rnor_1214
ATGTCTCTGGCAGATGAGCTCTTGGATGACCTTGAGGAGGCAGCAGAAGAGGAAGGAGGAAGCTACGGAGAAGAGAAGGA
GCCAGTAATTGAGGATATACAGGAGGAGACACAACTAGATCTTTCTGGAGATTCAGTCAAGAGCATTGCCAAGCTATGGG
ATAGCAAGATGTTTGCTGAGATCATGATGAAGATTGAGGAGTGTATCAGCAAACAGCCAAAGCTTCAGAAGTGATGGGAC
CAGTGGAGGCAGCCTCTGAGTACCGAGTCATTGTGGATGCCAACACCCTGACAGTGGAGATAGAAAACAAGCTGAACGTT
ATCTATAAATTCATCTGGGATAAATACTCGAAGAGATTCCCTGAACTAGAATCCTTGGTGCCCAATGCTCTGGATTACAT
TGGCAACAGTCAAGGAGCTGGGCAACAGCCTGGATAAGTGTAAGAACAATGAGAACCTCCAGCAGATCCTGGCCAATGCT
ATCATCATGGTTGTTAGTGTTGCAATCTCTACCACCCAGTGGCAGCAGCTGCGGGATGAGGAGCTAGAGTGGTTAGAGGA
GGCCTGTGACATGGCATTGAGCTGAATGCCTCCAAGCACCACATCTATGAGTACATGGAGTCCCAGATGTCCTTCATTGC
CCCCAGTTTGTCCATCATCATTGGAGCATCCATGGCTACCAAGATCATGGGTGTGGCCGGAGGGTTGACCAGCCTCTCTA
AGATGCCTGCCTGCAATATCATGCTGCTGGGAGCCCAGAGCAAGACACTGTCTGGCTTCTCTTCTACCTCAGTGCTGCCT
TACACTGGCTCATCTACCACAGTGACATCGTGCAGTCTTTGCCCCCAGATCTCCGGTGGAAGGCGGCCCATCTACTGGCT
GCCAAGTCTACACTAGCAGTTCGTGTGGACAGCTTCCATGAGAGCACAAAGGGAAGGTGGGCTATGAACTAAAAGATGAG
ATTGAGTACAAGTTTGACAAGTGGCAGGAGCCACCACCCCTT

Alignment

ORF - retro_rnor_1214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.13 %
• Parental protein coverage: 67.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSLADELLADLEEAAEEEEGGSYGEEEEEPAIEDVQEETQLDLSGDSVKSIAKLWDSKMFAEIMMKIEEY
          MSLADELL.DLEEAAEEE.GGSYGEE.E.P.IED.QEETQLDLSGDSVKSIAKLWDSKMFAEIMMKIEE.
Retrocopy MSLADELLDDLEEAAEEE-GGSYGEEKE-PVIEDIQEETQLDLSGDSVKSIAKLWDSKMFAEIMMKIEEC

Parental  ISKQ-AKASEVMGPVEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYI-RT
          ISKQ.AKASEVMGPVEAA.EYRVIVDAN.LTVEIEN.LN.I.KFI.DKYSKRFPELESLVPNALDYI..T
Retrocopy ISKQ<AKASEVMGPVEAASEYRVIVDANTLTVEIENKLNVIYKFIWDKYSKRFPELESLVPNALDYI>AT

Parental  VKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSDEELERLEEACDMAL-ELNASKHRIYEY
          VKELGNSLDKCKNNENLQQIL.NA.IMVVSV..STTQ.QQL.DEELE.LEEACDMAL.ELNASKH.IYEY
Retrocopy VKELGNSLDKCKNNENLQQILANAIIMVVSVAISTTQWQQLRDEELEWLEEACDMAL<ELNASKHHIYEY

Parental  VESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTLSGFSSTSVLPHTG-YIYH
          .ES.MSFIAP.LSIIIGAS.A.KIMGVAGGLT.LSKMPACNIMLLGAQ.KTLSGFSSTSVLP.TG..IYH
Retrocopy MESQMSFIAPSLSIIIGASMATKIMGVAGGLTSLSKMPACNIMLLGAQSKTLSGFSSTSVLPYTG<LIYH

Parental  SDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHEST-EGKVGYELKDEIERKFDKWQEPPPV
          SDIVQSLPPDLR.KAA.L.AAK.TLA.RVDSFHEST..GKVGYELKDEIE.KFDKWQEPPP.
Retrocopy SDIVQSLPPDLRWKAAHLLAAKSTLAVRVDSFHEST<KGKVGYELKDEIEYKFDKWQEPPPL

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	20.35 RPM
SRP017611_kidney	0.00 RPM	15.35 RPM
SRP017611_liver	0.00 RPM	9.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1214 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1214 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000006936	1 retrocopy	retro_ogar_2646,
Rattus norvegicus	ENSRNOG00000013504	1 retrocopy	retro_rnor_1214 ,