RetrogeneDB ID: retro_rnor_230

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:173525306..173525882(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000020393
• Aliases: Rhog, Arhg
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rac1
• Ensembl ID: ENSRNOG00000001068
• Aliases: None
• Description: Ras-related C3 botulinum toxin substrate 1 [Source:UniProtKB/Swiss-Prot;Acc:Q6RUV5]

Sequence

>retro_rnor_230
ATGCAGAGCATCAAGTGTGTGGTGGTGGGTGATGGGGCCGTAGGCAAGACGTGCCTTCTCATCTGCTATACAACTAATGC
CTTCCCCAAGGAATACATCCCCACTGTGTTCGACAATTACAGCGCCCAGAGTGCGGTTGATGGGCGCACCGTGAACCTAA
ACCTGTGGGACACTGCCGGCCAGGAGGAGTACGACCGCCTCCGCACCCTTTCCTACCCCCAGACCAACGTCTTCGTCATC
TGTTTCTCCATTGCCAGTCCACCCTCCTATGAGAACGTGAGGCACAAATGGCACCCAGAGGTGTGTCACCACTGCCCTGA
TGTGCCCATCCTCCTGGTGGGCACCAAGAAGGACCTCAGAGCCCAGCCTGATACCCTACGGCGCCTCAAGGAGCAGGGTC
AAGCGCCCATCACACCACAGCAGGGCCAGGCGCTGGCCAAGCAGATCCACGCTGTGCGCTACCTCGAGTGCTCAGCGCTG
CAGCAAGACGGTGTCAAGGAGGTGTTTGCCGAGGCTGTCCGGGCGGTGCTCAACCCAACACCGATAAAGCGTGGGCGGTC
CTGCATCCTCTTGTGA

Alignment

ORF - retro_rnor_230 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
          MQ.IKCVVVGDGAVGKTCLLI.YTTNAFP.EYIPTVFDNYSA...VDG..VNL.LWDTAGQE.YDRLR.L
Retrocopy MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRTVNLNLWDTAGQEEYDRLRTL

Parental  SYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYP
          SYPQT.VF.ICFS..SP.S.ENVR.KW.PEV.HHCP..PI.LVGTK.DLR...DT...LKE....PIT..
Retrocopy SYPQTNVFVICFSIASPPSYENVRHKWHPEVCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPITPQ

Parental  QGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
          QG.A.AK.I.AV.YLECSAL.Q.G.K.VF.EA.RAVL.P.P..KR.R.C.LL
Retrocopy QGQALAKQIHAVRYLECSALQQDGVKEVFAEAVRAVLNPTPI-KRGRSCILL

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	15.46 RPM	118.99 RPM
SRP017611_kidney	16.33 RPM	80.04 RPM
SRP017611_liver	11.90 RPM	47.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_230 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_230 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_28
Gorilla gorilla	retro_ggor_188
Pongo abelii	retro_pabe_21
Macaca mulatta	retro_mmul_210
Mus musculus	retro_mmus_234
Oryctolagus cuniculus	retro_ocun_43

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000136238	6 retrocopies	retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372, retro_mmus_234,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230 ,
Rattus norvegicus	ENSRNOG00000013536	1 retrocopy	retro_rnor_2062,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,