RetrogeneDB ID: retro_ocun_499

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:42977468..42977997(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022285
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_499
GGCTGCGGCTTCTTCCTGGAAATGACCACCTGGAACCTGCAAGCAGCAATTGAAGCCTATTATGACTTTGAAAGCCCAAG
TATCAGTGTGCCCTCCATGTCCTTTGTCGAAGATGTCACCATAGGAGCAGGGGAGTCAATTCCTCCTGATACTCAGTTTA
TAAAAACAGGGGAATCCAGAATCCTGGGGCAGAGGCCTGGCCTCCCGGGGTTTATCTCAAGTATGTGGGGGGAGACCAAT
CTGGACACGTGAACATGGTGACAGTGAGATCGCTAGAGCGCCAAGAGACTGCAGATGTCAGCGGCCAGGTGTGCAGCCCC
AAGCAGACAGGAATGTATCAGGGAGAGTGGGGACAAGCACTGCTACAGGGCTCTACTATGGCGATGTCATCTGGGTGATA
CTCAGGGTGGAGGTGGGTGGACTTTTAGGAGTAACACAGCAGCTGTCATCTTTTGAAACAGAGTTCAACACACAGCCGCA
TTGCAAGGTAGAAGGAAGCTCCAACCCATTTGCCTCTCCCCAAAGGAGC

Alignment

ORF - retro_ocun_499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.68 %
• Parental protein coverage: 61.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GCAFFLDMTNWNLQAAIGAYYDFESPNISVPSMSFVEDVTIGEGESIPPDTQFIKTWR-IQNSGAEAWPP
          GC.FFL.MT.WNLQAAI.AYYDFESP.ISVPSMSFVEDVTIG.GESIPPDTQFIKT...IQN.GAEAWPP
Retrocopy GCGFFLEMTTWNLQAAIEAYYDFESPSISVPSMSFVEDVTIGAGESIPPDTQFIKTGE<IQNPGAEAWPP

Parental  GVCLKYVGGDQFGHVNMVMVRSLEPQEIADVSVQMCSPSRAGMYQGQWRMC-TATGLYYGDVIWVILSVE
          GV.LKYVGGDQ.GHVNMV.VRSLE.QE.ADVS.Q.CSP...GMYQG.W....TATGLYYGDVIWVIL.VE
Retrocopy GVYLKYVGGDQSGHVNMVTVRSLERQETADVSGQVCSPKQTGMYQGEWGQA<TATGLYYGDVIWVILRVE

Parental  VGGLLGVTQQL-SFETEFNTQPHRKVEGNFNPFASPQRA
          VGGLLGVTQQL.SFETEFNTQPH.KVEG..NPFASPQR.
Retrocopy VGGLLGVTQQLSSFETEFNTQPHCKVEGSSNPFASPQRS

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	0.22 RPM	38.91 RPM
SRP017611_kidney	0.10 RPM	24.93 RPM
SRP017611_liver	0.00 RPM	31.14 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_499 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_499 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,