RetrogeneDB ID: retro_rnor_1494

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:54691491..54692044(+)
• Located in intron of: ENSRNOG00000013389

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rap1a
• Ensembl ID: ENSRNOG00000032463
• Aliases: Rap1a, RAP-1A, rap 1A
• Description: Ras-related protein Rap-1A [Source:UniProtKB/Swiss-Prot;Acc:P62836]

Sequence

>retro_rnor_1494
ATGCATGAGTACAAGCTAGTGGTCCTTGGTTAAGGAGGCATGGGAAAGTCTGATCTGACAGTTCAGTGTGTTCAGGTAAT
TTTATTTTGAAAAATATGACCCATCGATAGAAGATTCCTACATAAAGCAAGTCAAAGTAGATTGCCAACAGTGTATGCTG
GAAATCCTGGACACCTCAGGGACAGAACAATTTACAGCAATGAGGGATTTGTGTTTGAAGAATGGCCAAGGGTTTGCACT
AGTTTATTCAATTACAGCTCAGTCTACATTTAATGACTTACAAGACTTGACAGAACAGATTTTACGGGTTAACGACACAG
AAGCTGTTCCAATGATTTTGGTTGGCAATAAAAGTGACCTGGAAGATGAGCGGGTATTTAGCAAAGAACAAGACCAGGAT
TTAGCAAGACAATGGTGTAACTGTCCCTTTTTAGAATCTTCTGCAAAGTCAAAGATCAACGTTGATGAGATATTTTATGA
GCTGTTCAGACAGATAAATAGAAAAGCACCAGTGGAAAAGAAGAAGCCTAAAGGGAAATCATGTCTGCTGCTC

Alignment

ORF - retro_rnor_1494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGI-FVEKYDPTIEDSYRKQVEVDCQQCMLEILDTAGTEQFTAMRD
          M.EYKLVVLG.GG.GKS.LTVQ.VQ.I...EKYDP.IEDSY.KQV.VDCQQCMLEILDT.GTEQFTAMRD
Retrocopy MHEYKLVVLG*GGMGKSDLTVQCVQVI>YFEKYDPSIEDSYIKQVKVDCQQCMLEILDTSGTEQFTAMRD

Parental  LYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWC
          L..KNGQGFALVYSITAQSTFNDLQDL.EQILRV.DTE.VPMILVGNK.DLEDERV..KEQ.Q.LARQWC
Retrocopy LCLKNGQGFALVYSITAQSTFNDLQDLTEQILRVNDTEAVPMILVGNKSDLEDERVFSKEQDQDLARQWC

Parental  NCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCLLL
          NC.FLESSAKSKINV.EIFY.L.RQINRK.PVEKKKPK.KSCLLL
Retrocopy NCPFLESSAKSKINVDEIFYELFRQINRKAPVEKKKPKGKSCLLL

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	33.36 RPM
SRP017611_kidney	0.00 RPM	49.89 RPM
SRP017611_liver	0.00 RPM	26.09 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1494 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1494 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
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,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,