RetrogeneDB ID: retro_ocun_145

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 19:6830913..6831240(+)
• Located in intron of: ENSOCUG00000003519

Retrocopy information

• Ensembl ID: ENSOCUG00000022824
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: POLR3K
• Ensembl ID: ENSOCUG00000013608
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa (POLR3K), mRNA [Source:RefSeq mRNA;Acc:NM_001171411]

Sequence

>retro_ocun_145
CTGTTGCTCTTCTGCCCCGGCTGTGGGAACGGGCTGATCATGGAGGAGGGGCAGCGCTGCGACCGCTTCGCCTGCAACAC
CTGCCCCTACGTGCACAACATCACCCGCAAGGTCATAAACCAGAAGTATCCGAAGCTGAAAGAAGTAGACAACATGCTTG
GGGGAGCGGCCGCCTGGGAGAATGTTGACTCCACTGCAGAGCCGTGTCCCAAGTGCGAACATCCTCGTGCTTACTTCATG
CAGCTTCAGACGCGCTCTGCGGACAAGCCCATGACCACCTTCTACAAGTGCTGCAGCCCCCAGTGCGGGCACCGCTGGAG
GGACTAG

Alignment

ORF - retro_ocun_145 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLFCPGCGNGLIVEEGQRCHRFACNTCPYVHNITRKVTNRKYPKLKEVDDVLGGAAAWENVDSTAEPCP
          .LLFCPGCGNGLI.EEGQRC.RFACNTCPYVHNITRKV.N.KYPKLKEVD..LGGAAAWENVDSTAEPCP
Retrocopy LLLFCPGCGNGLIMEEGQRCDRFACNTCPYVHNITRKVINQKYPKLKEVDNMLGGAAAWENVDSTAEPCP

Parental  KCEHPRAYFMQLQTRSADEPMTTFYKCCSPQCGHRWRD
          KCEHPRAYFMQLQTRSAD.PMTTFYKCCSPQCGHRWRD
Retrocopy KCEHPRAYFMQLQTRSADKPMTTFYKCCSPQCGHRWRD

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	12.97 RPM
SRP017611_kidney	0.00 RPM	10.24 RPM
SRP017611_liver	0.00 RPM	3.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_145 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_145 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019715	1 retrocopy	retro_cfam_1881,
Callithrix jacchus	ENSCJAG00000011568	1 retrocopy	retro_cjac_2660,
Echinops telfairi	ENSETEG00000009989	2 retrocopies	retro_etel_1166, retro_etel_1543,
Felis catus	ENSFCAG00000009110	2 retrocopies	retro_fcat_1978, retro_fcat_409,
Homo sapiens	ENSG00000161980	1 retrocopy	retro_hsap_1861,
Myotis lucifugus	ENSMLUG00000015593	3 retrocopies	retro_mluc_1565, retro_mluc_1943, retro_mluc_341,
Oryctolagus cuniculus	ENSOCUG00000013608	1 retrocopy	retro_ocun_145 ,
Otolemur garnettii	ENSOGAG00000002526	2 retrocopies	retro_ogar_1101, retro_ogar_254,
Pan troglodytes	ENSPTRG00000007525	1 retrocopy	retro_ptro_1241,
Pteropus vampyrus	ENSPVAG00000000530	1 retrocopy	retro_pvam_928,
Sus scrofa	ENSSSCG00000007970	1 retrocopy	retro_sscr_1141,