RetrogeneDB ID: retro_ocun_1555

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018700:2340878..2341406(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STYX
• Ensembl ID: ENSOCUG00000029442
• Aliases: None
• Description: serine/threonine/tyrosine interacting protein [Source:HGNC Symbol;Acc:11447]

Sequence

>retro_ocun_1555
AAGGAATGGACCTATCCTATGAGGCGGGAGATGCAGGAAATTTTACATGGATTGTTCTTAGGTCCATATTCTTCTGCTAT
GAAAAGCAAGCTACCTATACTACAGAAACATGGAATAACCCATATAATTTGCATACAACAAAATATTGAAGCAAACTTTA
TTAAACCAAACTTTCAACAATTATTTAGGTATTTAGCCTTGGATATTGCAGATAAACCAGTTGAAAATATACTACATTTT
TTTCACTATGACTAAAGAATTTATTGATGGGAGCTTACTAACTGGAGGGAAAGTTCTTGTCCATGGAAATGTAGGGATCT
CCAGAAGTGCTGCCTTTGTTATTGCATACCTATGGAAACATTTGGAATGAAGTACGGAGATGCATTTGCTTATGTTCAAG
AAAGAAGATTTTGTATTAATCCTAATGTTGGATTTGAAAAGCAACTTCAGGAATATGAAGCAATTTATCTAGCAAAATTA
ACAATACAGATGATGTCACCACTTCAAATAGATCATTATCTGTTCATT

Alignment

ORF - retro_ocun_1555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 81.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEWTYPMRREMQEILPGLFLGPYSSAMKSKLPILQKHGITHIICIRQNIEANFIKPNFQQLFRYLVLDIA
          KEWTYPMRREMQEIL.GLFLGPYSSAMKSKLPILQKHGITHIICI.QNIEANFIKPNFQQLFRYL.LDIA
Retrocopy KEWTYPMRREMQEILHGLFLGPYSSAMKSKLPILQKHGITHIICIQQNIEANFIKPNFQQLFRYLALDIA

Parental  DNPVENIIR-FFPMTKEFIDGSLQTGGKVLVHGNAGISRSAAFVIAYL-METFGMKYRDAFAYVQERRFC
          D.PVENI...FF.MTKEFIDGSL.TGGKVLVHGN.GISRSAAFVIAYL.METFGMKY.DAFAYVQERRFC
Retrocopy DKPVENILH>FFTMTKEFIDGSLLTGGKVLVHGNVGISRSAAFVIAYL<METFGMKYGDAFAYVQERRFC

Parental  INPNVGFVHQLQEYEAIYLAKLTIQMMSPLQIERSLSV
          INPNVGF..QLQEYEAIYLAKLTIQMMSPLQI...L..
Retrocopy INPNVGFEKQLQEYEAIYLAKLTIQMMSPLQIDHYLFI

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	0.06 RPM	2.65 RPM
SRP017611_kidney	0.10 RPM	3.75 RPM
SRP017611_liver	0.00 RPM	1.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1555 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1555 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000029372	1 retrocopy	retro_mdom_44,
Mus musculus	ENSMUSG00000053205	1 retrocopy	retro_mmus_96,
Oryctolagus cuniculus	ENSOCUG00000029442	1 retrocopy	retro_ocun_1555 ,
Ochotona princeps	ENSOPRG00000016123	1 retrocopy	retro_opri_976,
Rattus norvegicus	ENSRNOG00000007956	1 retrocopy	retro_rnor_256,
Ictidomys tridecemlineatus	ENSSTOG00000014504	1 retrocopy	retro_itri_1365,
Vicugna pacos	ENSVPAG00000012229	1 retrocopy	retro_vpac_464,