RetrogeneDB ID: retro_rnor_872

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:23911242..23911596(+)
• Located in intron of: ENSRNOG00000046184

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rap1b
• Ensembl ID: ENSRNOG00000007048
• Aliases: None
• Description: Ras-related protein Rap-1b [Source:UniProtKB/Swiss-Prot;Acc:Q62636]

Sequence

>retro_rnor_872
GTTCAAGGAATTTTTGTTGAAAAATATGATCCTATGATAGAAGATTCTTATAGAAAGCAAGTTGAAGGAGATGCACAGCA
GTGTATGCTTGAAATCCTGGATACTGCAGGAACGGAGCAGTTTACAGCCATGAGAGATCTGTACATGAAGAACAGACAAG
GCTTTGTGTTGGTTTACTCCATCACAGCACAGTCGACATTTAATGACTTACAGGATCTAAGAGAGAAGATTCTTTGGGTT
AAAGACACTGACAATGTTCCAGAGATTCTGCTTGGTAATAAATGCGACTTGGAAGGTGAAAGCGTTGTAGGAAAGGAACA
AGGTCAGAACCTAGCAAGACAGTGGAACAACTGC

Alignment

ORF - retro_rnor_872 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.83 %
• Parental protein coverage: 64.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDL
          VQGIFVEKYDP.IEDSYRKQVE.DAQQCMLEILDTAGTEQFTAMRDLYMKN.QGF.LVYSITAQSTFNDL
Retrocopy VQGIFVEKYDPMIEDSYRKQVEGDAQQCMLEILDTAGTEQFTAMRDLYMKNRQGFVLVYSITAQSTFNDL

Parental  QDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWSNC
          QDLRE.IL.VKDTD.VP.IL.GNKCDLE.E.VVGKEQGQNLARQW.NC
Retrocopy QDLREKILWVKDTDNVPEILLGNKCDLEGESVVGKEQGQNLARQWNNC

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	0.36 RPM	53.13 RPM
SRP017611_kidney	0.21 RPM	101.46 RPM
SRP017611_liver	0.20 RPM	39.87 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_872 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_872 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_872 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Erinaceus europaeus	ENSEEUG00000010052	1 retrocopy	retro_eeur_327,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Microcebus murinus	ENSMICG00000013148	1 retrocopy	retro_mmur_116,
Macaca mulatta	ENSMMUG00000011442	2 retrocopies	retro_mmul_1151, retro_mmul_1863,
Oryctolagus cuniculus	ENSOCUG00000029552	5 retrocopies	retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872 ,
Rattus norvegicus	ENSRNOG00000016611	1 retrocopy	retro_rnor_2941,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,