RetrogeneDB ID: retro_ocun_808

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:78022423..78022984(+)
• Located in intron of: ENSOCUG00000006868

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTBD9
• Ensembl ID: ENSOCUG00000017258
• Aliases: None
• Description: BTB (POZ) domain containing 9 [Source:HGNC Symbol;Acc:21228]

Sequence

>retro_ocun_808
TGTGCGGCCATGGCAGAACCGCAACCTGCGTCCAGCGGCCTCACCGACGAGGCCGCCGCTAGCTGCTGCTCCGACGCGGA
CCCCAGCACCAAGGATTTTTTAATGCAACAGACCATGCTATGAATTAAGGATCCTAAGAAGTCATTGGATTTCTATACTA
GAATTCTTGGAATGACGCTAATCCAAAAATTAGATTTTCCTTCTATGAAATTTTCACTCTATTTCATGGCATATGAGGAT
AAAAATGACATCCCCAAAGATAAAAATGAAAGAGTAGCATGGGCATTTTCCAGAAAAGCTACCCTTGAGCTGACACATAA
TTGGGGCACTGAAGATGATGAGACCCAGAGCTACCACAGTGGCAATTCAGACCCTCGAGGATTTGGTCACATTGGAATTG
CTGTTCCTGATGTGTACGGCGCCTGTAAAAGATCTGAAGAACTGGGAGTCAAATTTGTGAAGAAACCAGACGATGGTAAA
ATGAAAGGCCTGGCATTTATTCGAGATCCTGATGGCTACTGGATTGAAATTTTGAATCCTAACACAATCACAAGTATCAT
T

Alignment

ORF - retro_ocun_808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CAAMAEPQPASSGLTDEAAASCCSDADPSTKDFLMQQTMLRIKDPKKSLDFYTRILGMTLIQKLDFPSMK
          CAAMAEPQPASSGLTDEAAASCCSDADPSTKDFLMQQTML.IKDPKKSLDFYTRILGMTLIQKLDFPSMK
Retrocopy CAAMAEPQPASSGLTDEAAASCCSDADPSTKDFLMQQTML*IKDPKKSLDFYTRILGMTLIQKLDFPSMK

Parental  FSLYFMAYEDKNDIPKDKNERVAWAFSRKATLELTHNWGTEDDETQSYHSGNSDPRGFGHIGIAVPDVYG
          FSLYFMAYEDKNDIPKDKNERVAWAFSRKATLELTHNWGTEDDETQSYHSGNSDPRGFGHIGIAVPDVYG
Retrocopy FSLYFMAYEDKNDIPKDKNERVAWAFSRKATLELTHNWGTEDDETQSYHSGNSDPRGFGHIGIAVPDVYG

Parental  ACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNTVTSII
          ACKR.EELGVKFVKKPDDGKMKGLAFI.DPDGYWIEILNPNT.TSII
Retrocopy ACKRSEELGVKFVKKPDDGKMKGLAFIRDPDGYWIEILNPNTITSII

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	0.11 RPM	71.52 RPM
SRP017611_kidney	0.10 RPM	86.05 RPM
SRP017611_liver	0.39 RPM	89.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_808 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_808 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000017258	2 retrocopies	retro_ocun_1911, retro_ocun_808 ,