RetrogeneDB ID: retro_ocun_776

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:120488820..120489713(-)
• Located in intron of: ENSOCUG00000025366

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZRANB2
• Ensembl ID: ENSOCUG00000004640
• Aliases: None
• Description: zinc finger, RAN-binding domain containing 2 [Source:HGNC Symbol;Acc:13058]

Sequence

>retro_ocun_776
ACCAAGAATTTCTGAGTCAGTGATGGGGACTGGATTTGCTGACAAAAAACTGTGGAAACTTAAACTTTGTTAGAAGAGCC
AGGTGTAATCAATGTGGTCAGGAGAAAATAACTAAAGCCAAGATGATACAAATGGAGGCACTGAAATAGGAAAGACTTTC
AGAAAAAAGCTGAGGCCTTTTTAGTGCCTATTACTGGCAGTGTAAGACTTGCAGTAATGTGAGCTGGTCCAAAAGATCAG
AATGTAACATGTGTAATATTCCAAAGTATGCTAAACTAGAAGAAAGAACAGGATATGGTGGTGGTTTTAATGAAAGAGAA
AATGTTTAATATATAGAAAGAGAAGAATCTGACAATGAATATAGTGAGTTTGGAGATAAGAAAAAAAGAGAGGAAAGGCA
GTTGGTCCTCCATCTATAGAGAAGAAGTTGAAGACAAAGCATCAGAAGGAGAATAAGAGGATGAGGATGAAGATCTTCCT
AAATATATATTAGATGAAGATGAGGATGAAGATGATGCTGATCTCTCAAAGTATAATCTTGATGCCAATGAAGAAGAAGA
CAGTAATAATAAAAAGAATTCTAGTAGATTAAGTCACTCAAAGCCTCAATCTTCACATTCACATTCTTCATCACACTCAT
CATCTCTCTTAAGTTCAAGGTCTAGGTCTAGGTTTCATTGAAGAATTTCTTCTGGTTCACAGTCAAGATCTTGTTCCAGT
TACAGAGAATGTTTGAGATCTTGTGGGTCGAAATCAAGATCCAGCTCCAGGTCCCACAGAGGCCCATCCTCCCCATGAAG
ATCTTCAAGTTCATCATCTTCTCCTGAGAAGAACAGAAAGAGAAATCATTCTAGATCTTCTTCATCTAGTGATAACAGAA
AAGACAAACAAGG

Alignment

ORF - retro_ocun_776 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.68 %
• Parental protein coverage: 91.54 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TKNFRVSDGDWICPDK-KCGNVNFARRTSCNRCGREKTTEAKMMKAGGTEIGKTLAEKSRGLFSANDWQC
          TKNF.VSDGDWIC..K..CGN.NF.RR..CN.CG.EK.T.AKM...........L.EKS.GLFSA..WQC
Retrocopy TKNF*VSDGDWIC*QK<NCGNLNFVRRARCNQCGQEKITKAKMIQMEALK*ER-LSEKS*GLFSAYYWQC

Parental  KTCSNVNWARRSECNMCNTPKYAKLEERTGYGGGFNERENVEYIEREESDGEYDEFGRKKKKY-RGKAVG
          KTCSNV.W..RSECNMCN.PKYAKLEERTGYGGGFNERENV.YIEREESD.EY.EFG..KKK..RGKAVG
Retrocopy KTCSNVSWSKRSECNMCNIPKYAKLEERTGYGGGFNERENV*YIEREESDNEYSEFG-DKKKR<RGKAVG

Parental  PASILK-EVEDKESEGEEEDEDEDLSKYKLDEDEDEDDADLSKYNLDASEEEDSSNKKKSSRRSRSKSRS
          P.SI.K.EVEDK.SEGE.EDEDEDL.KY..........ADLSKYNLDA.EEEDS.NKK.SSR.S.SK..S
Retrocopy PPSIEK<EVEDKASEGE*EDEDEDLPKYIXXXXXXXXXADLSKYNLDANEEEDSNNKKNSSRLSHSKPQS

Parental  SHSRSSSRSSSPSSSRSRSRSRSRSSSSSQSRSRSSSRERSRSRGSKSRSSSRSHRGSSSPRKRSYSSSS
          SHS.SSS.SSS..SSRSRSR...R.SS.SQSRS.SS.RE..RS.GSKSRSSSRSHRG.SSP.....SSSS
Retrocopy SHSHSSSHSSSLLSSRSRSRFH*RISSGSQSRSCSSYRECLRSCGSKSRSSSRSHRGPSSP*RS--SSSS

Parental  SSPERNRKRSRSRSSSSGDRK-KRRTR
          SSPE.NRKR..SRSSSS.D...KR.TR
Retrocopy SSPEKNRKRNHSRSSSSSDNR<KRQTR

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	0.11 RPM	76.88 RPM
SRP017611_kidney	0.00 RPM	44.39 RPM
SRP017611_liver	0.00 RPM	20.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_776 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_776 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_776 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006356	2 retrocopies	retro_cjac_2350, retro_cjac_4199,
Monodelphis domestica	ENSMODG00000000504	2 retrocopies	retro_mdom_1975, retro_mdom_443,
Oryctolagus cuniculus	ENSOCUG00000004640	2 retrocopies	retro_ocun_1170, retro_ocun_776 ,
Otolemur garnettii	ENSOGAG00000000485	4 retrocopies	retro_ogar_1274, retro_ogar_1841, retro_ogar_2843, retro_ogar_976,
Pan troglodytes	ENSPTRG00000000856	1 retrocopy	retro_ptro_3251,