RetrogeneDB ID: retro_rnor_2506

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:16680109..16680319(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1562351
• Ensembl ID: ENSRNOG00000042758
• Aliases: Tmem243, RGD1562351
• Description: None

Sequence

>retro_rnor_2506
TCTGCCAGGAGCCCAGACATTTGTTTACTTGGTAGAAGCTTAACATATTTGTGTATTCTAGTAACATTGTCCTGTGTTTT
CCTTTTCTCTCAGTTGTCAACCAAACAGCTAAATTTAGTGTTTGCTCTCTCTATGTCTTTGAGCAGCACCACTGCTTGCA
TACTTATCTATTAGTATCAACAAAAAAAAGTTTGGATTGAATTTTGAAAT

Alignment

ORF - retro_rnor_2506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.43 %
• Parental protein coverage: 59.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAKDRIINLVVGGLTTLLILVTLVSAFLFPQLPPKPLNIFFAVCISLSSITACILIYWYRQGDLEPKFRN
          SA....I.L....LT.L.ILVTL...FLF.QL..K.LN..FA...SLSS.TACILIY.Y........F.N
Retrocopy SARSPDICLLGRSLTYLCILVTLSCVFLFSQLSTKQLNLVFALSMSLSSTTACILIY*YQXXXVWIEF*N

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	4.53 RPM
SRP017611_kidney	0.00 RPM	21.07 RPM
SRP017611_liver	0.00 RPM	10.29 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2506 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2506 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004888	4 retrocopies	retro_chof_1660, retro_chof_175, retro_chof_1906, retro_chof_821,
Microcebus murinus	ENSMICG00000014707	1 retrocopy	retro_mmur_808,
Otolemur garnettii	ENSOGAG00000000023	2 retrocopies	retro_ogar_1800, retro_ogar_383,
Rattus norvegicus	ENSRNOG00000042758	1 retrocopy	retro_rnor_2506 ,
Sorex araneus	ENSSARG00000002439	1 retrocopy	retro_sara_32,
Tupaia belangeri	ENSTBEG00000007846	3 retrocopies	retro_tbel_2016, retro_tbel_2828, retro_tbel_4176,