RetrogeneDB ID: retro_ocun_1170

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:89825545..89826074(+)
• Located in intron of: None

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_1170
AGAAGAAAAAGAGGAAAGGCAGTTGGTCCTGCATCTATATTAAAAGAAGTTGAAGACAAAGAATCAGAGGGAGGATGAGG
ATGAAGATCTTTCTAAATATAAATTAGATGAGGATGAAGATGAAGATGATGCTGATCTCTCAAAATATAATCTTGATGCC
AGTGAAGAAGATAGCAGTAACAAAAAGAAGTCTAGTAGAGGGAGTCGCTCAAAGTCTTGATCTTCACTTTCACTGTCTTC
ATCACACTCATCCTCCCCCTCAAGTTCAAGGTCCAGGTCCAGATCCCGTTCAAGGAGTTCTTCCAGTTCGCAGTCAAGAT
CTCGTTCCAGTTCCAGAGAACATTCGCGATCTTGTGGGTCGAAATCAAGATCCAGCTCTAGGTCCCACAGGGGCTCCTCC
TCTTCCCCACGAAAAAGATCTTACTCAAGTTCATTGTCTTCTCCTGAGAGAAACAGAAAGAGAAGTCGTTCTAGATCTTC
TTCATCCTGTGATGGCAAAAAAAGATGAACAAGATCACGGTCACCCGAA

Alignment

ORF - retro_ocun_1170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 54.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKYRGKAVGPASILKEVEDKESEG-EEEDEDEDLSKYKLDEDEDEDDADLSKYNLDASEEEDSSNKKKSS
          ...RGKAVGPASILKEVEDKESEG..E......LSKYK.........ADLSKYNLDAS.EEDSSNKKKSS
Retrocopy RRKRGKAVGPASILKEVEDKESEG>DEDED---LSKYKXXXXXXXXXADLSKYNLDAS-EEDSSNKKKSS

Parental  RRSRSKSRSSHSRSSSRSSSPSSSRSRSRSRSRSSSSSQSRSRSSSRERSRSRGSKSRSSSRSHRG-SSS
          R.SRSKS.SS.S.SSS.SSSPSSSRSRSRSRSRSSSSSQSRSRSSSRE.SRS.GSKSRSSSRSHRG.SSS
Retrocopy RGSRSKS*SSLSLSSSHSSSPSSSRSRSRSRSRSSSSSQSRSRSSSREHSRSCGSKSRSSSRSHRGSSSS

Parental  PRKRSYSSSSSSPERNRKRSRSRSSSSGDRKKRRTRSRSPE
          PRKRSYSSS.SSPERNRKRSRSRSSSS.D.KKR.TRSRSPE
Retrocopy PRKRSYSSSLSSPERNRKRSRSRSSSSCDGKKR*TRSRSPE

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	0.17 RPM	76.88 RPM
SRP017611_kidney	0.10 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_1170 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1170 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,