RetrogeneDB ID: retro_ocun_1221

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:13270193..13270863(+)
• 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_1221
TTTGATTTGATGGATGCCAGAGCACGTGCTGATTGCATCAAAGAAATAGACCTCCCTAAGCAACTCAACCATCCAAATGT
GATTAAATACTATGCGTCATGTATTAAAGATAATGAATTAAATATAGTCTTGGAATTAGCAGACGCTGGTGACCTATTGA
GAATGATAAAGCATTTTAAGAAACAAGAGAGGTTAATTCCCGGGAGAACTGTCTGGAAGTACTTTGTGCAGCTCTGCAGT
GCCTTGGACCACGTGCATTTTCGCAGAGTCCTGCATAGAGATATCAAACCAGCTAATGTGTTCATTACAGCCACTGCAGT
GGTGAAACTTGGTGATCTTGGGTCTGGTGGTTTTTCAGCTTCAAGACCACAGCTGCACATTCCCTAGTGGGTAGACCTTA
TTACATGTCTCCACAGAGAATACATGAAAATGGGTACAACTTCAAATCTGACATCTGGTTTCTTGGCTGTCTACTATGTG
AGATGGCTGCATTACAGAGTCCTTTCTATGGTGACAAACTGAATTTATACTCACTGTGTGAGAAGATAGAACAGTGTGAC
TACTGCCTCTGCCTTCAGATCACTCTTCAGAAGAATTATGGCAGTGAGTTAACATGTGCATCCACCCCAATCTGGAGAAG
TGGCCAGACATCACCTACGTCTGTGACATA

Alignment

ORF - retro_ocun_1221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.07 %
• Parental protein coverage: 74.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDLMDAKARADCIKEIDLLKQLNHSNVIKCYASFIEDNELNIVLELADAGDLSRMIKHFKKQKRLIPERT
          FDLMDA.ARADCIKEIDL.KQLNH.NVIK.YAS.I.DNELNIVLELADAGDL.RMIKHFKKQ.RLIP.RT
Retrocopy FDLMDARARADCIKEIDLPKQLNHPNVIKYYASCIKDNELNIVLELADAGDLLRMIKHFKKQERLIPGRT

Parental  VWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVVKLGDLGLGR-FFSSKTTAAHSLVGTPYYMSPE
          VWKYFVQLCSAL.H.H.RRV.HRDIKPANVFITAT.VVKLGDLG.G..FFS.KTTAAHSLVG.PYYMSP.
Retrocopy VWKYFVQLCSALDHVHFRRVLHRDIKPANVFITATAVVKLGDLGSGG<FFSFKTTAAHSLVGRPYYMSPQ

Parental  RIHENGYNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDY-PPLPSDHYSEELRQLVNVCI
          RIHENGYNFKSDIW.LGCLL.EMAALQSPFYGDK.NLYSLC.KIEQCDY..PLPSDH.SEEL.Q.VN.CI
Retrocopy RIHENGYNFKSDIWFLGCLLCEMAALQSPFYGDKLNLYSLCEKIEQCDY<LPLPSDHSSEELWQ*VNMCI

Parental  NPDPEKRPDITYVYDV
          .P..EK.PDITYV.D.
Retrocopy HPNLEKWPDITYVCDI

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	27.87 RPM
SRP017611_kidney	0.00 RPM	71.15 RPM
SRP017611_liver	0.00 RPM	7.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1221 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1221 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,