RetrogeneDB ID: retro_ocun_629

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:1956070..1956385(-)
• Located in intron of: ENSOCUG00000027957

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM104A
• Ensembl ID: ENSOCUG00000003744
• Aliases: None
• Description: family with sequence similarity 104, member A [Source:HGNC Symbol;Acc:25918]

Sequence

>retro_ocun_629
TCCCTTCCACCAGCTGCCACGAGCAAGCGCCTGGGCTCCAGGCGAAGGAGAAGGAACAGCAACGCAGAGGAGAATCACCT
GTCCCCCCAGACCGCAAGGAGTAGCAGAAACCCTGTCTTCCAGGATTCCTGGGACACAGAGACAGCACCTGTGACGAAAA
AACAGTAGAGAAAACAGCCCAAGAGGAAACAAAGCATCCTCATGTCTTCAAGCAGTGGCAGCAGCAGCAGCGGCCTTCAC
ACTCAGGGAGAGCCACGGTCTGACAGCAGCATCCAGCCCACGCCTGCGCAGTCTGCCTTGCGCCAAGGCCCTCAC

Alignment

ORF - retro_ocun_629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 51.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLPPAAMSERLRPRKRRRNGNEEENHLPPQTKRSSRNPVFQDSWDTETVPVT-KNSKENRLRGNKA-FCA
          SLPPAA.S.RL..R.RRRN.N.EENHL.PQT.RSSRNPVFQDSWDTET.PVT.KNS.EN..RGNKA....
Retrocopy SLPPAATSKRLGSRRRRRNSNAEENHLSPQTARSSRNPVFQDSWDTETAPVT>KNSRENSPRGNKA<ILM

Parental  SSSSDSGGSSSSSSIHSPDRASGAESSLSQSMAGSSPN
          SSSS.S..SS.......P...S.......QS.....P.
Retrocopy SSSSGS-SSSGLHTQGEPRSDSSIQPTPAQSALRQGPH

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	5.13 RPM
SRP017611_kidney	0.00 RPM	4.46 RPM
SRP017611_liver	0.00 RPM	2.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_629 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_629 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_629 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
Ailuropoda melanoleuca	ENSAMEG00000002692	1 retrocopy	retro_amel_273,
Mus musculus	ENSMUSG00000041629	1 retrocopy	retro_mmus_786,
Oryctolagus cuniculus	ENSOCUG00000003744	1 retrocopy	retro_ocun_629 ,