RetrogeneDB ID: retro_rnor_1514

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:104987541..104987791(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1110058L19Rik
• Ensembl ID: ENSRNOG00000028087
• Aliases: None
• Description: RIKEN cDNA 1110058L19 gene [Source:MGI Symbol;Acc:MGI:1915252]

Sequence

>retro_rnor_1514
ATGGTCTCCATAATCCTTTCTGTATCACAGATGGCTTCCGTCTGGAGAGCAACAAGATCATCTCTTCTGAATCATTCTTT
GAGGAAAATGAGTTAGCAAGAAGGAAAGCCTGATCCTGTGGAAGCAAGCCCTTAAGAAGTCAAAGCTGCCTGTTGGTTGT
TTTGACTCACTGAACGACTCACCCGAGGAGAGATACCCACTGCAGAAGTTTCCAGATGATGTTAATCCGGTTACCAAAGG
AAAAGGTGGA

Alignment

ORF - retro_rnor_1514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 79.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVSTILSVSRMAFVWRATRSSLLNHSLRKKSSQEGKPEPS-KQALKKSKLPVGRFDSLDDSPEERDPLQK
          MVS.ILSVS.MA.VWRATRSSLLNHSLRK.S.QEGKP.P..KQALKKSKLPVG.FDSL.DSPEER.PLQK
Retrocopy MVSIILSVSQMASVWRATRSSLLNHSLRKMS*QEGKPDPV>KQALKKSKLPVGCFDSLNDSPEERYPLQK

Parental  FPDDVNPVTKEKGG
          FPDDVNPVTK.KGG
Retrocopy FPDDVNPVTKGKGG

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	7.33 RPM
SRP017611_kidney	0.00 RPM	8.65 RPM
SRP017611_liver	0.00 RPM	3.83 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1514 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1514 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1514 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002602	2 retrocopies	retro_cfam_268, retro_cfam_657,
Choloepus hoffmanni	ENSCHOG00000011410	6 retrocopies	retro_chof_176, retro_chof_1854, retro_chof_252, retro_chof_465, retro_chof_694, retro_chof_966,
Erinaceus europaeus	ENSEEUG00000011260	1 retrocopy	retro_eeur_539,
Echinops telfairi	ENSETEG00000011154	1 retrocopy	retro_etel_1362,
Felis catus	ENSFCAG00000026799	1 retrocopy	retro_fcat_986,
Rattus norvegicus	ENSRNOG00000028087	1 retrocopy	retro_rnor_1514 ,
Tupaia belangeri	ENSTBEG00000004344	2 retrocopies	retro_tbel_3788, retro_tbel_4408,
Tarsius syrichta	ENSTSYG00000001769	1 retrocopy	retro_tsyr_67,