RetrogeneDB ID: retro_rnor_2360

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:54480394..54480908(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gpx8
• Ensembl ID: ENSRNOG00000010461
• Aliases: Gpx8, RGD1307506
• Description: probable glutathione peroxidase 8 [Source:RefSeq peptide;Acc:NP_001099881]

Sequence

>retro_rnor_2360
TTGAAATTCCTGAAGCCAAGAATCAACATCTTCTATTCCTTTGAAGTGAAGGATGCCAAAGGAAGGATGGTATCTCTGGA
AAGTTCAAATCAAAGTTTCCCTAGTTATAAGAGTGGTTAGTGACTGCTGGTTCACAGACAAGAGTTATGTGACCCCCAGG
AAGCTGCAGAAGGAGTTTGTGCCCTATTACTTCAATGTACTGGCTTTCCTGTGCAATCAGTTTGGAGAATCAGAGTCTAA
GTCCAGCAAGAAGGTAGAATCCTTTGCCAGAAAAAAGCTATGAAGTCACATTTCCCATCTTCTCCAAGATTAAGATTTTA
GGGCTGGAAGCAGAACCTGCATTTAGATTTCTTATTGAGTTTTCCAAGTAGGAACCAAGGTGGAACTTTTGAAAATATCT
GGTCAACCCTGAGGGACACTAAGTAGTGAAGTTCTGGAGGCCAGAAGGACCCACTGAAGCCATCAGACCTCACATATCAC
AAATGATTAGCAAATCATTCTTAAAAAGAAAAAG

Alignment

ORF - retro_rnor_2360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LKFLKPRINSFYSFEVKDAKGRMVSLE-KFKGK-ASLVVNVASDCRFTDKSYETLRELHKEFGPYHFNVL
          LKFLKPRIN.FYSFEVKDAKGRMVSLE.KFK.K..SLV..V.SDC.FTDKSY.T.R.L.KEF.PY.FNVL
Retrocopy LKFLKPRINIFYSFEVKDAKGRMVSLE<KFKSK<VSLVIRVVSDCWFTDKSYVTPRKLQKEFVPYYFNVL

Parental  AFPCNQFGESEPKSSKEVESFAR-KNYGVTFPIFHKIKILGPEAEPAFRFLVDSSKKEPRWNFWKYLVNP
          AF.CNQFGESE.KSSK.VESFAR.K.Y.VTFPIF.KIKILG.EAEPAFRFL...SK.EPRWNF.KYLVNP
Retrocopy AFLCNQFGESESKSSKKVESFAR>KSYEVTFPIFSKIKILGLEAEPAFRFLIEFSK*EPRWNF*KYLVNP

Parental  EGQ-VVKFWRPEEPLEAIRPHVSQMIG-QIILKKKE
          EG..VVKFWRPE.P.EAIRPH.SQMI..QIILKKK.
Retrocopy EGH*VVKFWRPEGPTEAIRPHISQMIS<QIILKKKK

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	7.41 RPM
SRP017611_kidney	0.00 RPM	8.02 RPM
SRP017611_liver	0.00 RPM	1.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2360 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2360 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
Canis familiaris	ENSCAFG00000028869	1 retrocopy	retro_cfam_66,
Rattus norvegicus	ENSRNOG00000010461	1 retrocopy	retro_rnor_2360 ,
Tarsius syrichta	ENSTSYG00000012413	2 retrocopies	retro_tsyr_1170, retro_tsyr_2159,