RetrogeneDB ID: retro_rnor_2097

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:210252098..210252368(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aamdc
• Ensembl ID: ENSRNOG00000012584
• Aliases: Aamdc, RGD1561459
• Description: adipogenesis associated, Mth938 domain containing [Source:RefSeq peptide;Acc:NP_001101963]

Sequence

>retro_rnor_2097
AGTCCGGCTTGGGATTGGAGAGAAACAGGAACTGAGCATTCTCCTGGAGTGCAGCCAGCAGACATAAAGGAAGTTGCTGA
GAAGGGTGTACAGACTCTTGTGATTGGCAGAGGAATGAGCGAGGCCTTGAAGGTGCCTCCATCGACTGTGGAGTAGCTCG
AGAAACAAGGCATTGATGTGCGAGTCCTCCAGACAGAGCGGGCAGTGAAGGAGTACAATGCCTTGGTTGCCCAAGGCGTA
AGGGTAGGAGGTGTCTTCCACTCCACCTGC

Alignment

ORF - retro_rnor_2097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.22 %
• Parental protein coverage: 72.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRAWDWRETGTEHSPGVQPADVKEVAEKGVQTLVIGRGMSEALKVPPSTVEYLEKQGIDVRVLQTEQAVK
          S.AWDWRETGTEHSPGVQPAD.KEVAEKGVQTLVIGRGMSEALKVPPSTVE.LEKQGIDVRVLQTE.AVK
Retrocopy SPAWDWRETGTEHSPGVQPADIKEVAEKGVQTLVIGRGMSEALKVPPSTVE*LEKQGIDVRVLQTERAVK

Parental  EYNALAARGIRVGGVFHSTC
          EYNAL.A.G.RVGGVFHSTC
Retrocopy EYNALVAQGVRVGGVFHSTC

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	3.02 RPM
SRP017611_kidney	0.00 RPM	4.75 RPM
SRP017611_liver	0.00 RPM	5.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2097 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2097 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2097 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	ENSAMEG00000002128	1 retrocopy	retro_amel_1604,
Callithrix jacchus	ENSCJAG00000014890	1 retrocopy	retro_cjac_165,
Echinops telfairi	ENSETEG00000006423	1 retrocopy	retro_etel_187,
Felis catus	ENSFCAG00000007450	1 retrocopy	retro_fcat_8,
Loxodonta africana	ENSLAFG00000000518	1 retrocopy	retro_lafr_784,
Microcebus murinus	ENSMICG00000000300	2 retrocopies	retro_mmur_157, retro_mmur_424,
Mustela putorius furo	ENSMPUG00000015932	1 retrocopy	retro_mputfur_1468,
Rattus norvegicus	ENSRNOG00000012584	1 retrocopy	retro_rnor_2097 ,
Tarsius syrichta	ENSTSYG00000002262	1 retrocopy	retro_tsyr_1886,
Tursiops truncatus	ENSTTRG00000007111	1 retrocopy	retro_ttru_406,