RetrogeneDB ID: retro_rnor_542

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:254333650..254334153(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Phyh
• Ensembl ID: ENSRNOG00000018044
• Aliases: None
• Description: Phytanoyl-CoA dioxygenase, peroxisomal [Source:UniProtKB/Swiss-Prot;Acc:P57093]

Sequence

>retro_rnor_542
CCAGATTCTGGCAAGTAGACGCCCCGGCATCCCTTGCATCAGGATCTATACTATTTCCTCTTCCGATCCAGCAACCAAGT
TGTGCTTAGACAGCCTTGGAGCACATTGACAGAAACGACGGTTGTCTGGCTGTGCTCCCAGGCACCCACAAAGGCACTCT
GAAACCACATGATTACCCCAAGTGGGAGAGAGGAGTTAACAAACTGTACCATGGCATCCAAAACTATAAGCCGAACAGCA
CCCAGGTGTACGCAGTGATGGAGAAGGGCGACGCTGTTTTCTTCAATCCTCTGCTCATCCATGGATCTGGTCGAAACAAC
CCAAGGATTCATAAAGCAACTTCCTGCCATTCTGCCAGCTCTGACTGCAAGTATATCAACGGGAAGGGCACCAGTCAAGA
AAACGTCGCCAAGGGAGTTGCCGGGCTAGTAGAGAAACAGTATGGAGTCAAGGGAATCATGGACTTTAAGGATACTTGGG
TGTTTCGATGCCAACTTGTGAAA

Alignment

ORF - retro_rnor_542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.01 %
• Parental protein coverage: 50.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDSGKKTSRHPLHQDLHF-FPFRPSNLIVCAWTAMEHIDRNNGCLVVLPGTHKGPLKPHDYPKWEGGVNK
          PDSGK.T.RHPLHQDL...FP..P.....CA.TA.EHIDRN.GCL.VLPGTHKG.LKPHDYPKWE.GVNK
Retrocopy PDSGK*TPRHPLHQDLYY<FPL-PIQQPSCA*TALEHIDRNDGCLAVLPGTHKGTLKPHDYPKWERGVNK

Parental  MYHGIQDYDPDSPRVHLVMEKGDTVFFHPLLIHGSGRNRTQGFRKAISCHYGSSDCKYISVKGTSQENIA
          .YHGIQ.Y.P.S..V..VMEKGD.VFF.PLLIHGSGRN......KA.SCH..SSDCKYI..KGTSQEN.A
Retrocopy LYHGIQNYKPNSTQVYAVMEKGDAVFFNPLLIHGSGRNNPR-IHKATSCHSASSDCKYINGKGTSQENVA

Parental  REVIEIAEKRYGVQGALDFEDTWKFRCRLVK
          ..V....EK.YGV.G..DF.DTW.FRC.LVK
Retrocopy KGVAGLVEKQYGVKGIMDFKDTWVFRCQLVK

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	46.01 RPM
SRP017611_kidney	0.00 RPM	196.44 RPM
SRP017611_liver	0.00 RPM	887.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_542 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_542 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002160	1 retrocopy	retro_chof_334,
Cavia porcellus	ENSCPOG00000007582	1 retrocopy	retro_cpor_161,
Rattus norvegicus	ENSRNOG00000018044	1 retrocopy	retro_rnor_542 ,
Tursiops truncatus	ENSTTRG00000011113	1 retrocopy	retro_ttru_1844,