RetrogeneDB ID: retro_ocun_495

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:21539774..21540426(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF24
• Ensembl ID: ENSOCUG00000029679
• Aliases: None
• Description: zinc finger protein 24 [Source:HGNC Symbol;Acc:13032]

Sequence

>retro_ocun_495
ATGTCAGCACAGTCAGTGGAAGAAGATTCCATACGTATAATCCCAAATCCAGATGAAGAGGAAAAGTTCTGAGAGTGAAG
TTGGAGAAAGAGCCCGATGGTAAAGAGGGATAGAGTATCCCCTGGAATCATCTCCCTGACCCTAAGGTTTTCCGACAGCG
ATTCAGGCAGTTTGGATACCAGGACTCACCAGGACCATGTGAAGCTGTGAGCCAGCTCTGAGAACTTTGCCATCTGTGGC
TCAGGCCAGAGACCCACACAAAAGAACAAATATTGGAGTAGGTAGTGCTTCAGCAGTTTGTTGCTTTCCTACTGAAGAGC
TACAAACATGGGTTTGGGAGGATCATCCAGAGAATGGGGAGGAGGCAGTGACCGTGCTGGAGGACTTGGAGAGTAAACTT
GATGACCCTGGACAGCTGGTTTCTCTTCATCAGTGAAAGCAGGAAGTGCTTGTAGAAGAGATAGAGTCTCAAAAGAGGCT
CAAGGGTTACCAAGTTCTGAGCTTGATGCTGTGGTGAACCAACTCAAGTGGCCATCCTGGTAGCTCCATCCCCTGAGGCA
CTGTGATGATGATGCTAGGACTGAAAGTGGAGCACCAGCTCCAAAGCAGGAGATCCCTTCAGCAGCAGAATCTCATGAAG
TTCCTGGCACTC

Alignment

ORF - retro_ocun_495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSAQSVEEDSILIIPNAEEEEK-ILRVKLEEDPDGEEGSSIPWNHLPDPEVFRQRFRQFGYQDSPGPREA
          MSAQSVEEDSI.IIPN..EEEK..LRVKLE..PDG.EG.SIPWNHLPDP.VFRQRFRQFGYQDSPGP.EA
Retrocopy MSAQSVEEDSIRIIPNPDEEEK<VLRVKLEKEPDGKEG*SIPWNHLPDPKVFRQRFRQFGYQDSPGPCEA

Parental  VSQLRELCRLWLRPETHTKEQILELVVLEQFVAILPK-ELQTWVREHHPENGEEAVAVLEDLESELDDPG
          VSQL.ELC.LWLRPETHTKEQILE.VVL.QFVA.L.K.ELQTWV.E.HPENGEEAV.VLEDLES.LDDPG
Retrocopy VSQL*ELCHLWLRPETHTKEQILE*VVLQQFVAFLLK<ELQTWVWEDHPENGEEAVTVLEDLESKLDDPG

Parental  QPVSLRRRKREVLVEEIVSQ-EEAQGLPSSELDAVENQLKWASWELHSLRHCDDDARTENGALAPKQEIP
          Q.VSL...K.EVLVEEI.SQ..EAQGLPSSELDAV.NQLKW.SW.LH.LRHCDDDARTE.GA.APKQEIP
Retrocopy QLVSLHQ*KQEVLVEEIESQ<KEAQGLPSSELDAVVNQLKWPSW*LHPLRHCDDDARTESGAPAPKQEIP

Parental  S-QQNLRKFLAL
          S.QQNL.KFLAL
Retrocopy S>QQNLMKFLAL

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	0.06 RPM	26.77 RPM
SRP017611_kidney	0.00 RPM	34.06 RPM
SRP017611_liver	0.00 RPM	10.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_495 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_495 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000009322	1 retrocopy	retro_mmul_1374,
Mus musculus	ENSMUSG00000051469	1 retrocopy	retro_mmus_3388,
Oryctolagus cuniculus	ENSOCUG00000029679	1 retrocopy	retro_ocun_495 ,