RetrogeneDB ID: retro_rnor_165

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:85078646..85079315(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000000217
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Gsta4
• Ensembl ID: ENSRNOG00000030449
• Aliases: None
• Description: Glutathione S-transferase alpha-4 [Source:UniProtKB/Swiss-Prot;Acc:P14942]

Sequence

>retro_rnor_165
ATGGAAGCCAAACCCAAGCTCTACTACTTTCAAGGCAGGGGAAGGATGGAGTCAATCCGCTGGCTGCTGGCTACAGCTGG
AGTGGAGTTTGAAGAAGAATTTCTTGAGACGAGAGAACAATATGAGAAGTTGCAAAAGGATGGATGTCTGCTTTTTGGCC
AAGTCCCATTGGTGGAAATAGACGGGATGCTACTGACACAGACCAGAGCCATCCTCAGCTACCTGGCTGCCAAGCACAAC
TTGTATGGGAAGGACCTGAAGGAGAGAGTCAGGATTGACATGCATGCCGATGGCACCCAGGACCTGATGATGATGATTAT
CGGGGCTCCATTTAAAGCCCCTCAGGAGAAAGAAGAGAGCTGTGCTTTAGCAGTGAGGAGGGCTAAAACCGGTTACTTCC
CAGTGTTTGAAAAGATTTTAAAAGACCACGGAGAGGCATTTCTTGTTGGCAACCAACTCAGTTGGGCAGACATACAGCTA
CTAGAAGCCATTTTGATGGTGGAAGAAGTCAGTGCTCCTGTGCTGTCTGACTTCCCTCTGCTGCAGGCATTTAAGACAAG
AATCAGCAACATTCCTACAATTAAGAAGTTCCTGCAACCTGGAAGTCAGAGGAAGCCACCTCCAGATGGCCACTATGTTG
ACGTGGTCAGGACCGTCCTGAAGTTCTAG

Alignment

ORF - retro_rnor_165 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVKPKLYYFQGRGRMESIRWLLATAGVEFEEEFLETREQYEKLQKDGCLLFGQVPLVEIDGMLLTQTRA
          ME.KPKLYYFQGRGRMESIRWLLATAGVEFEEEFLETREQYEKLQKDGCLLFGQVPLVEIDGMLLTQTRA
Retrocopy MEAKPKLYYFQGRGRMESIRWLLATAGVEFEEEFLETREQYEKLQKDGCLLFGQVPLVEIDGMLLTQTRA

Parental  ILSYLAAKYNLYGKDLKERVRIDMYADGTQDLMMMIIGAPFKAPQEKEESLALAVKRAKNRYFPVFEKIL
          ILSYLAAK.NLYGKDLKERVRIDM.ADGTQDLMMMIIGAPFKAPQEKEES.ALAV.RAK..YFPVFEKIL
Retrocopy ILSYLAAKHNLYGKDLKERVRIDMHADGTQDLMMMIIGAPFKAPQEKEESCALAVRRAKTGYFPVFEKIL

Parental  KDHGEAFLVGNQLSWADIQLLEAILMVEEVSAPVLSDFPLLQAFKTRISNIPTIKKFLQPGSQRKPPPDG
          KDHGEAFLVGNQLSWADIQLLEAILMVEEVSAPVLSDFPLLQAFKTRISNIPTIKKFLQPGSQRKPPPDG
Retrocopy KDHGEAFLVGNQLSWADIQLLEAILMVEEVSAPVLSDFPLLQAFKTRISNIPTIKKFLQPGSQRKPPPDG

Parental  HYVDVVRTVLKF
          HYVDVVRTVLKF
Retrocopy HYVDVVRTVLKF

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	0.79 RPM	12.73 RPM
SRP017611_kidney	3.91 RPM	118.84 RPM
SRP017611_liver	1.75 RPM	42.23 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_165 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_165 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034823	2 retrocopies	retro_cjac_2783, retro_cjac_2841,
Otolemur garnettii	ENSOGAG00000031992	1 retrocopy	retro_ogar_2737,
Rattus norvegicus	ENSRNOG00000030449	1 retrocopy	retro_rnor_165 ,