RetrogeneDB ID: retro_ocun_628

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:128373902..128374262(+)
• Located in intron of: ENSOCUG00000017751

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000000958
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] 1 subunit C2 [Source:UniProtKB/TrEMBL;Acc:G1SEF1]

Sequence

>retro_ocun_628
ATGATGAGCGGACGGCCGGGCCGAGAGCCCTTAAAGTTCCTGCCTGATGAGGCCCGGAGCCTGCCGCCACCCAAGCTTAC
CGACCCGCGGCTGCTCTACTTCGGCTTCATGGGCTACTGCTCCGGCCTGCTTGATAACGCTCTCCGGCGGAGGCCTGTGA
CGATGGCCGGTTTGCATCGCCAGCTTTTATATGTTACTTCCTTTGTTTTTGCTGGCTATTATCTTTTAAAACGTCAAGAT
TATATGTATGCTGTGAGGGACCATGACATGTTTGGGTATATGAATTCACATCCAGAGGATTTTCCTGAAAAAGATAAGAA
AACTTACGGTGAAATTCTTGAAGAATTCCATCCTGTGCAT

Alignment

ORF - retro_ocun_628 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MMSGRPGREPLKFLPDEARSLPPPKLTDPRLLYFGFMGYCSGLLDNALRRRPVTMAGLHRQLLYVTSFVF
          MMSGRPGREPLKFLPDEARSLPPPKLTDPRLLYFGFMGYCSGLLDNALRRRPVTMAGLHRQLLYVTSFVF
Retrocopy MMSGRPGREPLKFLPDEARSLPPPKLTDPRLLYFGFMGYCSGLLDNALRRRPVTMAGLHRQLLYVTSFVF

Parental  AGYYLLKRQDYMYAVRDHDMFGYMNSHPEDFPEKDKKTYGEILEEFHPVH
          AGYYLLKRQDYMYAVRDHDMFGYMNSHPEDFPEKDKKTYGEILEEFHPVH
Retrocopy AGYYLLKRQDYMYAVRDHDMFGYMNSHPEDFPEKDKKTYGEILEEFHPVH

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	14.46 RPM
SRP017611_kidney	0.51 RPM	29.29 RPM
SRP017611_liver	0.15 RPM	8.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_628 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_628 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_628 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000029444	1 retrocopy	retro_fcat_337,
Mus musculus	ENSMUSG00000030647	2 retrocopies	retro_mmus_2851, retro_mmus_687,
Oryctolagus cuniculus	ENSOCUG00000000958	1 retrocopy	retro_ocun_628 ,
Tursiops truncatus	ENSTTRG00000007154	1 retrocopy	retro_ttru_1263,