RetrogeneDB ID: retro_rnor_646

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:240766939..240767767(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pwp1
• Ensembl ID: ENSRNOG00000005350
• Aliases: Pwp1, RGD1310705
• Description: periodic tryptophan protein 1 homolog [Source:RefSeq peptide;Acc:NP_001178806]

Sequence

>retro_rnor_646
ATGAATCGCAGCCGCCAAGTGACCTGCGTGGCCTGCGTCCGCCGCGGCGTGGCCAAAGAGACGCCAGACAAGGTAGAGCT
AAATAAAGAGGAAGTGAAACGTCTCATTGCTGAAGCAAAAGAAAAGTTACAAGAGGAAGGTGGGAGTGAGGAAGAGGAGG
CAGGCAGTCCTTCAGAAGATGGCAGAGAGCCCGGACCCAGGTCCAGTCTAGGGAGCAACTGGAGGATGGGGATCCACAAG
ACGACCACACACTGGACGACGATGAACTGGCCAAGTACGACGAAGAGGACAACCCAGATGCTGAGACCATTGGTGAATCT
CTGTTGGGTCTTACTGTCTAGGGCAGTAACGATCAGGGTCCATACGCCACCCTGAAAGACACAGAACAGTATGAGCGTGA
AGACTCCTTGATTAAACCGACTGGCAACCTCATCGTCTGTGGCCGTGCTGAACAAGGGCAGTGTAACTTAGAGGTGCACG
TGTACAATCAAGAAGAGGAGTCTTTCTATGTCCACCATGACATACTCCTGTCTGCATATCCTGAGTGTGGAATGGCTGAA
TTTTGATCCTAGCCCAGATGCGGCTACTGGAAATTACATTGCTGTGGGAAACATGACCCTTGTCATTGAGGGGTGGGACC
TGGATATCGTGGACTCTCTAGAACCAGTCTTCACACTGGGAGGCAAGCTTTCAAAAAAGAAGAAGAAGAAAGGGAAAAAG
AGTTCGTCAGCAGAAGGGCATACTGATGCTGTCCTTGACCTTTCCTGGAGTAAGACAGTCAGAAACGTGCTGGTGAGTGC
ATCAGCAGACAGCACTGTAATCCTGTGG

Alignment

ORF - retro_rnor_646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 56.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNRSRQVTCVAWVRRGVAKETPDKVELSKEEVKRLIAEAKEKLQEEGGSEEEEV-GSPSEDGMQRARVQA
          MNRSRQVTCVA.VRRGVAKETPDKVEL.KEEVKRLIAEAKEKLQEEGGSE.EE..G..S....QRAR.Q.
Retrocopy MNRSRQVTCVACVRRGVAKETPDKVELNKEEVKRLIAEAKEKLQEEGGSE-EEE<GRQSFRRWQRARTQV

Parental  RPTEPLEDGDPQDDRTLDDDELAEYDLDNYDQEDNPDAETIGESLLGLTVYGSNDQDPYVTLKDTEQYEH
          ...E.LEDGDPQDD.TL.DD......L..YD.EDNPDAETIGESLLGLTV.GSNDQ.PY.TLKDTEQYE.
Retrocopy QSREQLEDGDPQDDHTL-DDD----ELAKYDEEDNPDAETIGESLLGLTV*GSNDQGPYATLKDTEQYER

Parental  EDFLIKPTDNLIVCGRAEQEQCNLEVHVYNQEEESFYVHHDILLSA-YPLSVEWLNFDPSPDAATGNYIA
          ED.LIKPT.NLIVCGRAEQ.QCNLEVHVYNQEEESFYV.H...L.....LSVEWLNFDPSPDAATGNYIA
Retrocopy EDSLIKPTGNLIVCGRAEQGQCNLEVHVYNQEEESFYV-HHDILLS>HILSVEWLNFDPSPDAATGNYIA

Parental  VGNMTPVIEVWDLDIVDSLEPVFTLGSKLSKKKKKKGKKSSSAEGHTDAVLDLSWNKTVRNVLASASADS
          VGNMT.VIE.WDLDIVDSLEPVFTLG.KL...........SSAEGHTDAVLDLSW.KTVRNVL.SASADS
Retrocopy VGNMTLVIEGWDLDIVDSLEPVFTLGGKLXXXXXXXXXXXSSAEGHTDAVLDLSWSKTVRNVLVSASADS

Parental  TVILW
          TVILW
Retrocopy TVILW

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	0.14 RPM	11.93 RPM
SRP017611_kidney	0.00 RPM	17.17 RPM
SRP017611_liver	0.00 RPM	8.74 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_646 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_646 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_646 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000015544	1 retrocopy	retro_mmul_688,
Macaca mulatta	ENSMMUG00000031574	1 retrocopy	retro_mmul_687,
Mus musculus	ENSMUSG00000001785	2 retrocopies	retro_mmus_1600, retro_mmus_3074,
Otolemur garnettii	ENSOGAG00000011940	2 retrocopies	retro_ogar_2999, retro_ogar_3444,
Rattus norvegicus	ENSRNOG00000005350	1 retrocopy	retro_rnor_646 ,
Tursiops truncatus	ENSTTRG00000011036	1 retrocopy	retro_ttru_540,