RetrogeneDB ID: retro_rnor_195

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:21073666..21074125(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000003606
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Mgst3
• Ensembl ID: ENSRNOG00000004245
• Aliases: None
• Description: microsomal glutathione S-transferase 3 [Source:RefSeq peptide;Acc:NP_001178523]

Sequence

>retro_rnor_195
ATGGCTGTCCTCTCTAAGGAATATGGATTCGTGCTTCTCACTGGTGCCGCCAGCTTTATGATGGTGCTCCACCTAGCCAT
CAACCTGGGCAAAGCCCGCAAGAAGTACAAGATAGAGTACCCTGTCATGTACAGCACAGATCCTGAGAATGGGTATATGT
TCAGTTGCATTCAGCGCGCCCACCAGAACACGTTGGAGGTGTACCCTCCCTTCCTATTCTTCCTAACCGTGGGAGGTGTT
TACCACCCGCGCATAGCTTCTGGCCTGGGCGTGGCGTGGATTATTGGGCGAGTTCTTTACGCATATGGCTACTACACAGG
AGACCCTAGCAAGCGATATCAAGGAGCTGTGAGCTCTCTTGCCCTCTTTGCCCTGATGGGCACAACCGTGTGCTCTGCTT
TCCAGCATCTCGGCTGGATTAAACCCGGCCTAGGCAGTGGGTCCAGATCCTGCCACTGA

Alignment

ORF - retro_rnor_195 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVLSKEYGFVLLTGAASFVMVLHLAINVGKARKKYKVEYPVMYSTDPENGHMFNCIQRAHQNTLEVYPP
          MAVLSKEYGFVLLTGAASF.MVLHLAIN.GKARKKYK.EYPVMYSTDPENG.MF.CIQRAHQNTLEVYPP
Retrocopy MAVLSKEYGFVLLTGAASFMMVLHLAINLGKARKKYKIEYPVMYSTDPENGYMFSCIQRAHQNTLEVYPP

Parental  FLFFLTVGGVYHPRIASGLGVAWIIGRVLYAYGYYTGDPSKRYRGAVSSLALFALMGTTVCSAFQHLGWI
          FLFFLTVGGVYHPRIASGLGVAWIIGRVLYAYGYYTGDPSKRY.GAVSSLALFALMGTTVCSAFQHLGWI
Retrocopy FLFFLTVGGVYHPRIASGLGVAWIIGRVLYAYGYYTGDPSKRYQGAVSSLALFALMGTTVCSAFQHLGWI

Parental  KPGLGSGSRSCH
          KPGLGSGSRSCH
Retrocopy KPGLGSGSRSCH

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	0.14 RPM	31.20 RPM
SRP017611_kidney	0.42 RPM	100.14 RPM
SRP017611_liver	0.13 RPM	37.79 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_195 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_195 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006658	1 retrocopy	retro_amel_1210,
Canis familiaris	ENSCAFG00000013353	1 retrocopy	retro_cfam_35,
Choloepus hoffmanni	ENSCHOG00000012723	2 retrocopies	retro_chof_1872, retro_chof_356,
Echinops telfairi	ENSETEG00000003507	3 retrocopies	retro_etel_1328, retro_etel_1527, retro_etel_1544,
Mustela putorius furo	ENSMPUG00000003817	1 retrocopy	retro_mputfur_1251,
Mus musculus	ENSMUSG00000026688	1 retrocopy	retro_mmus_2709,
Oryctolagus cuniculus	ENSOCUG00000010376	1 retrocopy	retro_ocun_270,
Procavia capensis	ENSPCAG00000015774	2 retrocopies	retro_pcap_385, retro_pcap_393,
Rattus norvegicus	ENSRNOG00000004245	1 retrocopy	retro_rnor_195 ,
Tupaia belangeri	ENSTBEG00000005299	2 retrocopies	retro_tbel_2989, retro_tbel_752,