RetrogeneDB ID: retro_ocun_723

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:126681069..126681407(+)
• Located in intron of: ENSOCUG00000025555

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLMO1
• Ensembl ID: ENSOCUG00000022237
• Aliases: None
• Description: slowmo homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:24639]

Sequence

>retro_ocun_723
ATGAAAACCTGGAGCTCAGAACACGTGGTATTTGGGCATCCATAGGACAAGGTGACTAAGATCACCATGAGGAGGTATCT
GAACCCAATAACCCAGGCATAGTAGGTGAGGACATGCTGGAGAGTGGCATGTGGTGGCATGGGCGGCTTCACAGCCTGTG
CCTGCTCAGCACAAAGTGGGGGCTACCTGGCCTTTTGTAAGCAATTTTGGGAACCAGCAGGGCTTTGACATACATCAAAT
AGCATTCTGTTGTAGATCCAATGGAAAAGAAAATGGAAGTCTGATCCACCAATATCCCACTCACAAATTTTGTGTCAGTG
AGAAGCTGGTATATACAC

Alignment

ORF - retro_ocun_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 65.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKIWSSEHV-FGHPWDTVIKAAMRKYPNPM-NPCVVGVDVLERGVDGRGRLHSLRLLSTEWGLPSLVRAI
          MK.WSSEHV.FGHP.D.V.K..MR.Y.NP..NP..VG.D.LE.G....GRLHSL.LLST.WGLP.L..AI
Retrocopy MKTWSSEHVVFGHP*DKVTKITMRRYLNPI<NPGIVGEDMLESGMWWHGRLHSLCLLSTKWGLPGLL*AI

Parental  LGTSRTLTYIKEHSVVDPAEKKMELCSTNITLTNLVSVNERLVY
          LGTSR.LTYIK.HSVVDP.EKKME..STNI.LTN.VSV......
Retrocopy LGTSRALTYIK*HSVVDPMEKKMEV*STNIPLTNFVSVRSWYIH

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	5.30 RPM
SRP017611_kidney	0.00 RPM	2.03 RPM
SRP017611_liver	0.00 RPM	0.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_723 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_723 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012800	2 retrocopies	retro_amel_1395, retro_amel_330,
Mus musculus	ENSMUSG00000024530	1 retrocopy	retro_mmus_1332,
Oryctolagus cuniculus	ENSOCUG00000005621	8 retrocopies	retro_ocun_1944, retro_ocun_1954, retro_ocun_455, retro_ocun_486, retro_ocun_549, retro_ocun_619, retro_ocun_775, retro_ocun_926,
Oryctolagus cuniculus	ENSOCUG00000022237	1 retrocopy	retro_ocun_723 ,
Procavia capensis	ENSPCAG00000001084	1 retrocopy	retro_pcap_66,