RetrogeneDB ID: retro_rnor_2059

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:63537435..63537832(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rhebl1
• Ensembl ID: ENSRNOG00000021571
• Aliases: None
• Description: GTPase RhebL1 [Source:UniProtKB/Swiss-Prot;Acc:Q7TNZ5]

Sequence

>retro_rnor_2059
GAGTTCCTGGAAGGCTACAATCCTACAGTGGAGAATACTTACAGCAAGCCAGTGACTCTTGGCAAAGATGAGTTTCACCT
ACATCTGGTGGACACAGCAGGACAGGATGAATGCAGCATTCTGCCCTATTCCTTCATCACTGGGGTCCATGGTTACATGC
TTGTGTACTCTTGTTACCTCCCTGCACAGCTTCCAAATCGTTAAGAACCTGTACCAAAAGCTACACGAAGTCCATGGTAA
AACACGGCTGCCAGTGCTGCTTGTGGGGAATAAGGCAGATCTCTGTGCAGACAGAGAGGTGCAGGCAGCTGAAGGGAAGA
AGCCAGCAGAGTCCTGGGGTGCAACGTTTATGGAGTCATCTGCACGGGATAATCAGCTAACTCAGGACATCTTCATC

Alignment

ORF - retro_rnor_2059 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.97 %
• Parental protein coverage: 72.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFLKGYDPTVENTYSKTVTLGKDEFHLHLVDTAGQDKYSILPYSFIIGVHGYVLVYN-VTSLRSFQIVKN
          EFL.GY.PTVENTYSK.VTLGKDEFHLHLVDTAGQD..SILPYSFI.GVHGY.LVY..VTSL.SFQIVKN
Retrocopy EFLEGYNPTVENTYSKPVTLGKDEFHLHLVDTAGQDECSILPYSFITGVHGYMLVYS>VTSLHSFQIVKN

Parental  LYQKLQEGHGKTRLPVLLVGNKADLSADREVQAVEGKKLAESWGATFMESSARDNQLIQDIFI
          LYQKL.E.HGKTRLPVLLVGNKADL.ADREVQA.EGKK.AESWGATFMESSARDNQL.QDIFI
Retrocopy LYQKLHEVHGKTRLPVLLVGNKADLCADREVQAAEGKKPAESWGATFMESSARDNQLTQDIFI

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	5.03 RPM
SRP017611_kidney	0.00 RPM	0.56 RPM
SRP017611_liver	0.00 RPM	0.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2059 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2059 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2059 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002998	1 retrocopy	retro_cpor_1328,
Erinaceus europaeus	ENSEEUG00000008514	2 retrocopies	retro_eeur_338, retro_eeur_528,
Oryctolagus cuniculus	ENSOCUG00000016881	1 retrocopy	retro_ocun_1802,
Otolemur garnettii	ENSOGAG00000013477	1 retrocopy	retro_ogar_2338,
Pan troglodytes	ENSPTRG00000004897	1 retrocopy	retro_ptro_115,
Rattus norvegicus	ENSRNOG00000021571	1 retrocopy	retro_rnor_2059 ,