RetrogeneDB ID: retro_ocun_1726

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018825:68800..69298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEK7
• Ensembl ID: ENSOCUG00000011419
• Aliases: None
• Description: NIMA-related kinase 7 [Source:HGNC Symbol;Acc:13386]

Sequence

>retro_ocun_1726
AGAGAACTGTGGAAGTACTTTTTGCAGCTCTACAGTGCCTTGGAACACATGCATTCTCGAAGAGTCATGCATAGAGATAT
CAAACCAGCTAATGTGTTCATTACAGCCACTGGAGTGGTAAAACTTGGTGATCTTGGGCTTGGCTGGTTTTCCAGCTCCA
AGACCACAGCTACACATTCTTTAGTGGGCACATTTTATTGCATGTCTCCAGAGAGAATACGTGAAAATGGATACAACTTC
AAATCTGACATCTGGTCTCTTGGCTGTCTACTATATGACATGGCTGCATTCCAGAGTCTTTTCTATGGTGACAAAATTAA
TTTATACTCACTGTGTAAGAAGATAGAACCATGCAGCTACTCACATCTGCCTTCAGAGCACTATTTAGAAGAATTACGGC
AGTTATTTAATATGTGCATCAACCCCAATCTGGAGAAGTGGCCGGACATCACCTATGTCTATGACATAGTGAAGAGAATG
CATTTGTGCACCGCAAGC

Alignment

ORF - retro_ocun_1726 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.13 %
• Parental protein coverage: 54.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTVWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVVKLGDLGLGRFFSSKTTAAHSLVGTPYYMSP
          R..WKYF.QL.SALEHMHSRRVMHRDIKPANVFITATGVVKLGDLGLG.F.SSKTTA.HSLVGT.Y.MSP
Retrocopy RELWKYFLQLYSALEHMHSRRVMHRDIKPANVFITATGVVKLGDLGLGWFSSSKTTATHSLVGTFYCMSP

Parental  ERIHENGYNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNVCI
          ERI.ENGYNFKSDIWSLGCLLY.MAA.QS.FYGDK.NLYSLCKKIE.C.Y..LPS.HY.EELRQL.N.CI
Retrocopy ERIRENGYNFKSDIWSLGCLLYDMAAFQSLFYGDKINLYSLCKKIEPCSYSHLPSEHYLEELRQLFNMCI

Parental  NPDPEKRPDITYVYDVAKRMHACTAS
          NP..EK.PDITYVYD..KRMH.CTAS
Retrocopy NPNLEKWPDITYVYDIVKRMHLCTAS

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	0.44 RPM	27.87 RPM
SRP017611_kidney	0.10 RPM	71.15 RPM
SRP017611_liver	0.15 RPM	7.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1726 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1726 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1726 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000007338	2 retrocopies	retro_mmur_1034, retro_mmur_1147,
Oryctolagus cuniculus	ENSOCUG00000011419	2 retrocopies	retro_ocun_1221, retro_ocun_1726 ,
Tarsius syrichta	ENSTSYG00000004270	1 retrocopy	retro_tsyr_2093,