RetrogeneDB ID: retro_ocun_1479

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:68835032..68835513(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF330
• Ensembl ID: ENSOCUG00000014580
• Aliases: None
• Description: zinc finger protein 330 [Source:HGNC Symbol;Acc:15462]

Sequence

>retro_ocun_1479
ATGCCTAAAAAAAGACTGGTGCAAGGAAAAAGGCCGAAAACTGCCAGGAACGTGAAAAACAACTAAGAGCCTCTGGAAGC
ACTGTAGATTTAGCTAAACACCCGTGTAATGTTCAATGGAAATGTGACAAGTGTCAGAGATGGCAGAATAGAGCATTTGG
CTACTTTTGTAATTCTGTACAGAAGTTGCCAATCTGTGCACAGTGTGGGAAACCAAAAAGCATGAGGAAATCTGATTGTG
TGAGAAGCATGCTGGTGTGTATGGTACTGGCCTGGCAATGGTGGTGCATGTGACCTCTGTGAAGCTTGGGTGTGCCCTGT
AGGAAATGCTCAGTACACATGCCCGTGCCTGCCCTCTTACTGATGCTGAGTGTGTTCCTTGTAAACCAGGTATATGGGAT
CTTGGAGGCAGAAGAGTCAGTTGCTCTTTTTGCCATAATTTTCTCTGCGAGGATGATCAATTTGAACATCAAGCCATTTG
T

Alignment

ORF - retro_ocun_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 51.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPKK-KTGARKKAENRREREKQLRASRSTVDLAKHPCNASMECDKCQRRQKNRAFCYFCNSVQKLPICAQ
          MPKK.KTGARKKAEN..EREKQLRAS.STVDLAKHPCN....CDKCQR.Q.NRAF.YFCNSVQKLPICAQ
Retrocopy MPKK<KTGARKKAENCQEREKQLRASGSTVDLAKHPCNVQWKCDKCQRWQ-NRAFGYFCNSVQKLPICAQ

Parental  CGKTKCMMKSSDCVI-KHAGVYSTGLAMV-GAICDFCEAWVCHG-RKC-LSTHACACPLTDAECVECERG
          CGK.K.M.KS.DCV..KHAGVY.TGLAMV.GA.CD.CEAWVC...RKC.LSTHA.ACPLTDAECV.C..G
Retrocopy CGKPKSMRKS-DCVR<KHAGVYGTGLAMV<GA-CDLCEAWVCPV<RKC<LSTHARACPLTDAECVPCKPG

Parental  VWDHGGRIFSCSFCHNFLCEDDQFEHQASC
          .WD.GGR..SCSFCHNFLCEDDQFEHQA.C
Retrocopy IWDLGGRRVSCSFCHNFLCEDDQFEHQAIC

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	25.22 RPM
SRP017611_kidney	0.00 RPM	26.15 RPM
SRP017611_liver	0.00 RPM	10.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1479 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1479 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
Mus musculus	ENSMUSG00000031711	1 retrocopy	retro_mmus_344,
Oryctolagus cuniculus	ENSOCUG00000014580	1 retrocopy	retro_ocun_1479 ,
Sus scrofa	ENSSSCG00000009052	1 retrocopy	retro_sscr_1043,