RetrogeneDB ID: retro_rnor_2808

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:65062219..65062526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kxd1
• Ensembl ID: ENSRNOG00000019971
• Aliases: None
• Description: KxDL motif-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5M853]

Sequence

>retro_rnor_2808
TTCATGAACCATATGTGGTGTGCCTTGGTGGATGTGAAATGCGACCCTGACTGCATCTTCCATGGGACCCTGAAGGGGAG
CTGTCCTGGCAGCACCTAGAGGCTTGAAAGCACATCTTGGAGCATTCGGTCCTGGAGGACAAAGATAAAGACCCTATTCT
GCCCAGTATCACCACAACCATGAGCACCTTGGAGCAGAGCATTGACTTCTGTGATACCAACACTGACATTGTCTAACCAT
CCCTCAGTCCTGGTTTTAAGGACCTATCACACATGCAACCTGGTTCCCTGCAATCATTGTACATTCA

Alignment

ORF - retro_rnor_2808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.94 %
• Parental protein coverage: 58.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FMHHTR-TLVDMKRDLDSIFRRIRTLKG-KLARQHPEAFSHIPEGSLLEDEDEDPVPPSITTTIATSEQS
          FM.H....LVD.K.D.D.IF....TLKG..L..QH.EA..HI.E.S.LED.D.DP..PSITTT..T.EQS
Retrocopy FMNHMWCALVDVKCDPDCIFHG--TLKG<ELSWQHLEA*KHILEHSVLEDKDKDPILPSITTTMSTLEQS

Parental  TGSCDTSPDTASPSFSPGFEDLSHIRPGS-PAINGHS
          ...CDT..D...PS.SPGF.DLSH..PGS.PAI..HS
Retrocopy IDFCDTNTDIV*PSLSPGFKDLSHMQPGS<PAIIVHS

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	22.50 RPM
SRP017611_kidney	0.00 RPM	24.77 RPM
SRP017611_liver	0.00 RPM	36.58 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2808 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2808 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010545	1 retrocopy	retro_btau_689,
Echinops telfairi	ENSETEG00000003390	2 retrocopies	retro_etel_1213, retro_etel_2129,
Macropus eugenii	ENSMEUG00000013150	1 retrocopy	retro_meug_2148,
Monodelphis domestica	ENSMODG00000003489	1 retrocopy	retro_mdom_1623,
Mus musculus	ENSMUSG00000055553	6 retrocopies	retro_mmus_1117, retro_mmus_3557, retro_mmus_799, retro_mmus_800, retro_mmus_802, retro_mmus_804,
Rattus norvegicus	ENSRNOG00000019971	2 retrocopies	retro_rnor_2808 , retro_rnor_812,