RetrogeneDB ID: retro_ocun_72

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018886:398517..399222(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026584
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000022833
• Aliases: None
• Description: None

Sequence

>retro_ocun_72
ATGAGCAGCGGCTACAGCAGCCTGGAGGAGGACGCCGAGGACTTCTTCACCGCCAGGACCTCCTTCTTCCGGAGAGCGCC
TCAGGGCAAGCCCCGCGCGGGCCAGCAAGATGTGGAGAAAGAGAAGGAAACTCACAATTACCTCAGCAAAGAGGAAATAA
AAGAGAAAGTTCATAAGTACAATTTGGCAGTCACAGACAAGTTGAAAATGACCTTGAATTCAAACGGGATTTACACTGGC
TTCATTAAAGTGCAGATGGAACTCTGCAAACCCACCCAGATGTCGGGGAAGCTCGCGCCTGGCAGCAACGGCTGTATGAA
CACGCTTCATATCAGCAGCACAAACACTGTCGGGGAAGTGATTGAGGCCCTGCTCAAAAAGTTCCTCGTGACCGAGAGCC
CTGCCAAGTTTGCACTTTATAAGCGTTGTCACAGGGAAGACCAAGTCTACGCCTGCAAGCTGTCAAACCGGGAGCATCCA
CTGTACCTGCGTTTGGTGGCAGGGCCCAGAACAGACACACTTAGCTTTGTTCTTCGTGAACATGAAATCGGAGAGTGGGA
AGCCTTCAGTCTTCCAGAGCTGCAGAACTTCGTGCGCTTGCTGGACAAAGAAGAAGACGAGCAGCTGCAGAGCCTGAGGC
GGCGCTACTCTGCCTACAGACAGAAGCTGGAAGAGGCCCTGGGCGAGGGCTGGAAGCCCAGGTAG

Alignment

ORF - retro_ocun_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.46 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVEKEKETHNYLSKEEIKEKVHKYNLAVTDKLKMTLNSNGIYTGFIKVQMELCKPTQTSGKLAPGSNGCM
          DVEKEKETHNYLSKEEIKEKVHKYNLAVTDKLKMTLNSNGIYTGFIKVQMELCKPTQ.SGKLAPGSNGCM
Retrocopy DVEKEKETHNYLSKEEIKEKVHKYNLAVTDKLKMTLNSNGIYTGFIKVQMELCKPTQMSGKLAPGSNGCM

Parental  NTLHISSTNTVGEVIEALLKKFLVTESPAKFALYKRCHREDQVYACKLSDREHPLYLRLVAGPRTDTLSF
          NTLHISSTNTVGEVIEALLKKFLVTESPAKFALYKRCHREDQVYACKLS.REHPLYLRLVAGPRTDTLSF
Retrocopy NTLHISSTNTVGEVIEALLKKFLVTESPAKFALYKRCHREDQVYACKLSNREHPLYLRLVAGPRTDTLSF

Parental  VLREHEIGEWEAFSLPELQNFLRMLDKEEDEQLQSLRRRYSAYRHKLEEALGEGWKP
          VLREHEIGEWEAFSLPELQNF.R.LDKEEDEQLQSLRRRYSAYR.KLEEALGEGWKP
Retrocopy VLREHEIGEWEAFSLPELQNFVRLLDKEEDEQLQSLRRRYSAYRQKLEEALGEGWKP

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	0.61 RPM	4.30 RPM
SRP017611_kidney	1.11 RPM	7.09 RPM
SRP017611_liver	1.08 RPM	7.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_72 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_72 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_72 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
Myotis lucifugus	ENSMLUG00000009170	1 retrocopy	retro_mluc_2315,
Oryctolagus cuniculus	ENSOCUG00000022833	1 retrocopy	retro_ocun_72 ,
Otolemur garnettii	ENSOGAG00000016553	1 retrocopy	retro_ogar_449,