RetrogeneDB ID: retro_ocun_1955

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:111139855..111140365(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf106
• Ensembl ID: ENSOCUG00000024862
• Aliases: None
• Description: chromosome 6 open reading frame 106 [Source:HGNC Symbol;Acc:21215]

Sequence

>retro_ocun_1955
ATGGAGGGCATGGACGTGGACCTGGACCCGGAGCTGATGCAGAAGTTCAGCTGCCTGGGCACCACCGACAAGGACGTGCT
CATCTCCGAGTTCCAGAGGCTGCTCGGCTTCCAGCTCAACCCGGCCAGCTGCGCCTTCTTCCTGGACATGACCAACTGGA
ACCTGCAAGCAGCAATTGGAGCCTATTATGACTTTGAGAGCCCAAATATCAGTGTGCCCTCCATGTCCTTTGTTGAAGAT
GTCACCATAGGAGAAGGGGAATCAATTCTTCCTGATACTCAGTTTATAAAAACATAGTGGATCCAGAATTCTGGGGCAGA
GGCCTGGCCTCCAGGGGTTTGTCTTAAGTATGTCAGGGGAGACCAGTTTGGACATGTGAACATGGTGATGGTGAGATCGC
TAGAGCCCCAAGAGATTGCAGGTGTCATCGTCCAGATGTGCAGCCCCAGCAGAGCAGGAATGTATCAGGGACAGTGGCGG
ATGTGCACTGCTACAGGACTCTACTATGGA

Alignment

ORF - retro_ocun_1955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.88 %
• Parental protein coverage: 59.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGMDVDLDPELMQKFSCLGTTDKDVLISEFQRLLGFQLNPAGCAFFLDMTNWNLQAAIGAYYDFESPNI
          MEGMDVDLDPELMQKFSCLGTTDKDVLISEFQRLLGFQLNPA.CAFFLDMTNWNLQAAIGAYYDFESPNI
Retrocopy MEGMDVDLDPELMQKFSCLGTTDKDVLISEFQRLLGFQLNPASCAFFLDMTNWNLQAAIGAYYDFESPNI

Parental  SVPSMSFVEDVTIGEGESIPPDTQFIKTWRIQNSGAEAWPPGVCLKYVGGDQFGHVNMVMVRSLEPQEIA
          SVPSMSFVEDVTIGEGESI.PDTQFIKT..IQNSGAEAWPPGVCLKYV.GDQFGHVNMVMVRSLEPQEIA
Retrocopy SVPSMSFVEDVTIGEGESILPDTQFIKT*WIQNSGAEAWPPGVCLKYVRGDQFGHVNMVMVRSLEPQEIA

Parental  DVSVQMCSPSRAGMYQGQWRMCTATGLYYG
          .V.VQMCSPSRAGMYQGQWRMCTATGLYYG
Retrocopy GVIVQMCSPSRAGMYQGQWRMCTATGLYYG

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	0.83 RPM	38.91 RPM
SRP017611_kidney	0.20 RPM	24.93 RPM
SRP017611_liver	0.15 RPM	31.14 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1955 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1955 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Oryctolagus cuniculus	ENSOCUG00000024862	2 retrocopies	retro_ocun_1955 , retro_ocun_499,
Rattus norvegicus	ENSRNOG00000038883	2 retrocopies	retro_rnor_1748, retro_rnor_1749,
Tursiops truncatus	ENSTTRG00000007822	4 retrocopies	retro_ttru_1601, retro_ttru_1738, retro_ttru_1896, retro_ttru_827,