RetrogeneDB ID: retro_rnor_1598

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:2529150..2529827(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000042806
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gstk1
• Ensembl ID: ENSRNOG00000016484
• Aliases: Gstk1, GST13-13, GSTkappa
• Description: Glutathione S-transferase kappa 1 [Source:UniProtKB/Swiss-Prot;Acc:P24473]

Sequence

>retro_rnor_1598
ATAGGGTGGGTACCACTTGCCCTGGAACTGTTCTATGATGTGCTGCCCCCTTACACCTGGCTGGGTTTTGAAATCCTATG
CAGATACCAACACCTCTAGAATATCAAGCCCAAGTTGTGTCCTGCTTTAATTGCTGGAATTATGAAAGACAGAGGAAACC
AACCACCAGCTATGGTTCCCTGCAAAGGCCAGTATATATTTAAAGAGATTCCTCTCTTGAAGAAGCTCTTTCAGGTTCCC
ATCAGCATACCCAAGGATTTCTTTGGTGAGAGTGTTAAGAAAGGAAGTATAAATGCCATGCTCTTCCTCACCGCTGTGAG
CATGGAGCAACCAGAGTTGCTGGAGAAGGTGTCCAGAGAGCTATGGTTGTGTGTTTGGTCTCAAGATGATGATATCACAG
AGTCCCAGAACATTCTGGCTGCTGCAGAGAGGGCTGGAATGTCCACAGCACAGGCCCAACGTTTTCTAGAGAAGATCCCC
CCAGAACCGGTGAAGAACAAGCTCAGGGAGGCTACTGAGACAGCCTGCAAATATGGGGCCGTTGAGCTGCCCACCACTGT
TGGCCATGAGGATGGTAAAACCTACATGGTATTTGGGTCTGACTGCATGGAGTTGCTAGTTATCTACTGGGAGAGAAGTG
GATGGGCCCTGTGCCTCCAACCCTGAATGGAGGACTT

Alignment

ORF - retro_rnor_1598 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGPAPRVLELFYDVLSPYSWLGFEVLCRYQHLWNIKLKLRPALLAGIMKDSGNQPPAMVPHKGQYILKEI
          .G..P..LELFYDVL.PY.WLGFE.LCRYQHL.NIK.KL.PAL.AGIMKD.GNQPPAMVP.KGQYI.KEI
Retrocopy IGWVPLALELFYDVLPPYTWLGFEILCRYQHL*NIKPKLCPALIAGIMKDRGNQPPAMVPCKGQYIFKEI

Parental  PLLKQLFQVPMSVPKDFFGEHVKKGTVNAMRFLTAVSMEQPEMLEKVSRELWMRIWSRDEDITESQNILS
          PLLK.LFQVP.S.PKDFFGE.VKKG..NAM.FLTAVSMEQPE.LEKVSRELW...WS.D.DITESQNIL.
Retrocopy PLLKKLFQVPISIPKDFFGESVKKGSINAMLFLTAVSMEQPELLEKVSRELWLCVWSQDDDITESQNILA

Parental  AAEKAGMATAQAQHLLNKISTELVKSKLRETTGAACKYGAFGLPTTVAHVDGKTYMLFGSDRMELL-AYL
          AAE.AGM.TAQAQ..L.KI..E.VK.KLRE.T..ACKYGA..LPTTV.H.DGKTYM.FGSD.MELL..YL
Retrocopy AAERAGMSTAQAQRFLEKIPPEPVKNKLREATETACKYGAVELPTTVGHEDGKTYMVFGSDCMELL<SYL

Parental  LGEKWMGPVPPTLNARL
          LGEKWMGPVPPTLN..L
Retrocopy LGEKWMGPVPPTLNGGL

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	0.22 RPM	8.70 RPM
SRP017611_kidney	0.07 RPM	37.12 RPM
SRP017611_liver	0.47 RPM	45.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1598 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1598 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000007274	1 retrocopy	retro_fcat_807,
Mustela putorius furo	ENSMPUG00000000713	1 retrocopy	retro_mputfur_1401,
Mus musculus	ENSMUSG00000029864	1 retrocopy	retro_mmus_1859,
Rattus norvegicus	ENSRNOG00000016484	1 retrocopy	retro_rnor_1598 ,
Sus scrofa	ENSSSCG00000016466	1 retrocopy	retro_sscr_1071,