RetrogeneDB ID: retro_rnor_1459

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:44033728..44034129(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Emg1
• Ensembl ID: ENSRNOG00000012828
• Aliases: Emg1, Grcc2f
• Description: probable ribosome biogenesis protein NEP1 [Source:RefSeq peptide;Acc:NP_001101358]

Sequence

>retro_rnor_1459
GAGAGGTCCTGACTGGGGCAGGGAGAACACACAGAGGCTATAAGGCTCATTGTAGTGATTTAAGATGCTAGTCTGGAGAC
AGTGGAGGATGGGTAAAGATACCAGCTACTCAACTGCCACAAGAACAAATTTATGCTGCTGAAGAGTAGGCAGGACTCTA
AGAAAGTGAGATAAGACATTGCCCAACTGAACCTCCTGATGCCGATGGAGAGTTCACTGAACAGAGCTGTCCTGCTACAT
GGTTGATTCATGCACAGAAGCTTGTATTGAGTAAAGTGAACCCCAGGCATCCGTTCTCAGGATCTTTGATCCCTTTTATG
GTCCTCATTGTTCAACTTTTACATAAACTCATCATCCAGGTAGCTAGTGGCTCTCAGAATCTTTTGAAGGTAACCTGTAA
T

Alignment

ORF - retro_rnor_1459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.01 %
• Parental protein coverage: 54.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRPRLGAGSKCGGRRLIVVLEGASLETVKVGKTYELLNCDKHKSMLLKNGRDPGEVRPDITHQSLLMLMD
          .R..LG.G......RLIVV...ASLETV..G..Y.LLNC.K.K.MLLK...D...VR.DI....LLM.M.
Retrocopy ERS*LGQGEHTEAIRLIVVI*DASLETVEDG*RYQLLNCHKNKFMLLKSRQDSKKVR*DIAQLNLLMPME

Parental  SPLNRAGLLQ-VYIHTQKNVLIEVN-PQTRIPRTFDRFCG-LMVQLLHKLSVRAADGPQKLLKVIKN
          S.LNRA.LL....IH.QK.VL..VN.PQ....R.FD.F.G.L.VQLLHKL....A.G.Q.LLKV..N
Retrocopy SSLNRAVLLH<WLIHAQKLVLSKVN<PQASVLRIFDPFYG>LIVQLLHKLIIQVASGSQNLLKVTCN

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	16.25 RPM
SRP017611_kidney	0.00 RPM	15.70 RPM
SRP017611_liver	0.00 RPM	8.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1459 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1459 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013753	1 retrocopy	retro_amel_1924,
Callithrix jacchus	ENSCJAG00000007120	1 retrocopy	retro_cjac_2960,
Gorilla gorilla	ENSGGOG00000004287	1 retrocopy	retro_ggor_3077,
Macropus eugenii	ENSMEUG00000000831	1 retrocopy	retro_meug_1299,
Myotis lucifugus	ENSMLUG00000009196	1 retrocopy	retro_mluc_737,
Macaca mulatta	ENSMMUG00000010207	1 retrocopy	retro_mmul_671,
Nomascus leucogenys	ENSNLEG00000005080	1 retrocopy	retro_nleu_501,
Otolemur garnettii	ENSOGAG00000006975	2 retrocopies	retro_ogar_2971, retro_ogar_945,
Pongo abelii	ENSPPYG00000004215	1 retrocopy	retro_pabe_2924,
Rattus norvegicus	ENSRNOG00000012828	1 retrocopy	retro_rnor_1459 ,