RetrogeneDB ID: retro_ocun_1643

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018737:1297359..1297949(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CERS5
• Ensembl ID: ENSOCUG00000012843
• Aliases: None
• Description: ceramide synthase 5 [Source:HGNC Symbol;Acc:23749]

Sequence

>retro_ocun_1643
CAGTTCACTTTTTATTGATGTATATTCTGCTACAGAATGAGGTTTCTCTGGTCATCACCTTGGTTCTGGGACAGGTGGCA
CTGCTGGCCCAGCTAACTATATCAGCCCCTTTCAAGTGCACTTCACAAATATGTCATGGAGTTGGCCTTCTTGTTTTCTC
AATTTGTAGACATTAAAAGAAAGGGCTTTCTGATTATGTTTGCACATCTCTTGGCCACCACTGGGCTTAGCACCTTCTTC
TACATCAACGACGTGGTCCAGTGGGAACTCTGGTCATGTGTGTCTGCGTGATGCCTCAGACTTCTCACCGGAGGCAGCCA
AGCTAGCAAATGATGCCAGGTACCAGCGGCTCTGCGACAGCCTTCCTGTGACATCAGGGGTGTTTCTGTGGTCGCTCATC
TAGGAATCTGTCCATTTTGCATTCTCGACACGACCCTCGTTGAGAGCTGGGAGCTGATCGGCCCTATCCTTCCTGGTGGC
TCTTCAACCGGCTCCTCCCGATCCTACAGGTTCTGCATGTCCTCTGGTCCTACCTTATTGCACGAATTGCTTTCAAAGCC
TTGATCCACAGAAAGGTGGCCAAGGACAAT

Alignment

ORF - retro_ocun_1643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.34 %
• Parental protein coverage: 54.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RFTFYLCIFCYGIRFLWSSPWFWDTRQCWHSYPYQPLSSGLYYYYVMELAFYWSLMFSQFIDIKRKDFLI
          .FTFY.CIFCY..RFLWSSPWFWD...CW.S..YQPLSS.L..Y.VMELAF.....FSQF.DIKRK.FLI
Retrocopy QFTFY*CIFCYRMRFLWSSPWFWDRWHCWPS*LYQPLSSALHKY-VMELAF----LFSQFVDIKRKGFLI

Parental  MFVHHLAT-IGLITFSYINNMVRVGTLVMCLHDASDFLLEAAKLANYAKYQRLCDTLFVI-FSAVFVVTR
          MF.H.LAT..GL...S.............CL.DASDF..EAAKLAN.A.YQRLCD.L.V.....V.VV..
Retrocopy MFAHLLAT>LGLAPSSTSTTWSSGNSGHVCLRDASDFSPEAAKLANDARYQRLCDSLPVT<IRGVSVVAH

Parental  LGIYPFWILNTTLFESWEMIGP-YPSWWLFNGLLLILQVLHVIWSYLIARIAFKALIRGKVSKDD
          LGI.PF.IL.TTL.ESWE.IGP.YPSWWLFN.LL.ILQVLHV.WSYLIARIAFKALI..KV.KD.
Retrocopy LGICPFCILDTTLVESWELIGP<YPSWWLFNRLLPILQVLHVLWSYLIARIAFKALIHRKVAKDN

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	0.00 RPM	52.65 RPM
SRP017611_kidney	0.00 RPM	24.73 RPM
SRP017611_liver	0.00 RPM	10.56 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1643 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1643 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000012843	1 retrocopy	retro_ocun_1643 ,
Otolemur garnettii	ENSOGAG00000004668	1 retrocopy	retro_ogar_392,
Pteropus vampyrus	ENSPVAG00000006713	1 retrocopy	retro_pvam_591,
Sus scrofa	ENSSSCG00000024932	1 retrocopy	retro_sscr_1195,