RetrogeneDB ID: retro_ocun_1111

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:106460289..106460528(-)
• Located in intron of: ENSOCUG00000005236

Retrocopy information

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

Parental gene information

• Parental gene symbol: AS3MT
• Ensembl ID: ENSOCUG00000000626
• Aliases: None
• Description: arsenic (+3 oxidation state) methyltransferase [Source:HGNC Symbol;Acc:17452]

Sequence

>retro_ocun_1111
ACCTGTGGTAACAGTGCGTTCCTGCTCACCAAGCAGGTGCTGAAGGCCTGCCAGAGCCCGGAGCTGCAAGGTCGGGCAGC
TCAAGATGTGGCACTGCGGGGAGAAGCCATCTTGCACCCAGGAGGTAGTTTAGAGAAAATGACAATGATAAATACTCATT
TCAATACCAGCCAGAAGCTGTTCAGAACAATGTTGAGCAGTTGTCAGATCCATAGGACCAGTTGAGTCATCTGTTGAAA

Alignment

ORF - retro_ocun_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.02 %
• Parental protein coverage: 75.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TCGTDVIALTKQVLKGSRSSELLGQAARNMVLQEDAILHSEDSLRKMAIITTH-LQYQQEAIQKNVEQSS
          TCG.....LTKQVLK...S.EL.G.AA....L...AILH...SL.KM..I.TH..QYQ.EA.Q.NVEQ.S
Retrocopy TCGNSAFLLTKQVLKACQSPELQGRAAQDVALRGEAILHPGGSLEKMTMINTH<FQYQPEAVQNNVEQLS

Parental  DLQDQLNHLLK
          D..DQL.HLLK
Retrocopy DP*DQLSHLLK

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	9.82 RPM
SRP017611_kidney	0.00 RPM	25.74 RPM
SRP017611_liver	0.00 RPM	19.96 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1111 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1111 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000000626	1 retrocopy	retro_ocun_1111 ,
Procavia capensis	ENSPCAG00000000867	1 retrocopy	retro_pcap_406,